From ef445ac96cc9adb49413e40983f909bb07b8c451 Mon Sep 17 00:00:00 2001
From: Judy Yao <xiaozheng.yao@nih.gov>
Date: Thu, 3 Aug 2023 09:25:44 -0400
Subject: [PATCH] update version

---
 client/LDlink.js | 11096 +++++++++++++++++++++++++--------------------
 1 file changed, 6112 insertions(+), 4984 deletions(-)

diff --git a/client/LDlink.js b/client/LDlink.js
index 3fabc802..3a939270 100644
--- a/client/LDlink.js
+++ b/client/LDlink.js
@@ -1,19 +1,543 @@
-var ldlink_version = "Version 5.6.4";
-
+var ldlink_version = 'Version 5.6.5';
 
 // var restService = {protocol:'http',hostname:document.location.hostname,fqn:"nih.gov",port:9090,route : "LDlinkRestWeb"}
 // var restServerUrl = restService.protocol + "://" + restService.hostname + "/"+ restService.route;
-var restService = {protocol: window.location.protocol, hostname: window.location.host, pathname: window.location.pathname, route: 'LDlinkRestWeb'}
-var restServerUrl = restService.protocol + "//" + restService.hostname + restService.pathname + restService.route;
-
-var dropdowns = ["assoc-chromosome", "assoc-position", "assoc-p-value"];
-
-var populations={AFR:{fullName:"African",subPopulations:{YRI:"Yoruba in Ibadan, Nigera",LWK:" Luhya in Webuye, Kenya",GWD:" Gambian in Western Gambia",MSL:"  Mende in Sierra Leone",ESN:"  Esan in Nigera",ASW:" Americans of African Ancestry in SW USA",ACB:"  African Carribbeans in Barbados"}},AMR:{fullName:"Ad Mixed American",subPopulations:{MXL:"  Mexican Ancestry from Los Angeles, USA",PUR:" Puerto Ricans from Puerto Rico",CLM:" Colombians from Medellin, Colombia",PEL:" Peruvians from Lima, Peru"}},EAS:{fullName:"East Asian",subPopulations:{CHB:" Han Chinese in Bejing, China",JPT:" Japanese in Tokyo, Japan",CHS:" Southern Han Chinese",CDX:" Chinese Dai in Xishuangbanna, China",KHV:"  Kinh in Ho Chi Minh City, Vietnam"}},EUR:{fullName:"European",subPopulations:{CEU:" Utah Residents from North and West Europe",TSI:"  Toscani in Italia",FIN:"  Finnish in Finland",GBR:" British in England and Scotland",IBS:"  Iberian population in Spain"}},SAS:{fullName:"South Asian",subPopulations:{GIH:"  Gujarati Indian from Houston, Texas",PJL:"  Punjabi from Lahore, Pakistan",BEB:"  Bengali from Bangladesh",STU:"  Sri Lankan Tamil from the UK",ITU:" Indian Telugu from the UK"}}};
-var ldPairData={corr_alleles:["rs2720460(A) allele is correlated with rs11733615(C) allele","rs2720460(G) allele is correlated with rs11733615(T) allele"],haplotypes:{hap1:{alleles:"AC",count:"155",frequency:"0.686"},hap2:{alleles:"GC",count:"40",frequency:"0.177"},hap3:{alleles:"GT",count:"29",frequency:"0.128"},hap4:{alleles:"AT",count:"2",frequency:"0.009"}},snp1:{allele_1:{allele:"A",count:"157",frequency:"0.695"},allele_2:{allele:"G",count:"69",frequency:"0.305"},coord:"chr4:104054686",rsnum:"rs2720460"},snp2:{allele_1:{allele:"C",count:"195",frequency:"0.863"},allele_2:{allele:"T",count:"31",frequency:"0.137"},coord:"chr4:104157164",rsnum:"rs11733615"},statistics:{chisq:"67.271",d_prime:"0.9071",p:"0.0",r2:"0.2977"},two_by_two:{cells:{c11:"155",c12:"2",c21:"40",c22:"29"},total:"old - 227"}};
-var ldhapData={footer:[{Count:127,Frequency:.588,Haplotype:"GCATGGCGTTGGGG"},{Count:40,Frequency:.1852,Haplotype:"GGGGAGCGTTGGGG"},{Count:23,Frequency:.1065,Haplotype:"GCGGAGCGTTGGGG"},{Count:11,Frequency:.0509,Haplotype:"TGGGAGCGTTGGGG"},{Count:8,Frequency:.037,Haplotype:"GCATAGCGTTGGGG"},{Count:7,Frequency:.0324,Haplotype:"TGGGGATAGCAAAG"}],rows:[{Alleles:"G=0.917, T=0.083",Coord:"chr4:104050980",RS:"rs2720457",Haplotypes:["G","G","G","T","G","T"]},{Alleles:"C=0.732, G=0.269",Coord:"chr4:104052963",RS:"rs2720458",Haplotypes:["C","G","C","G","C","G"]},{Alleles:"A=0.625, G=0.375",Coord:"chr4:104055748",RS:"rs2720461",Haplotypes:["A","G","G","G","A","G"]},{Alleles:"T=0.625, G=0.375",Coord:"chr4:104056210",RS:"rs2720462",Haplotypes:["T","G","G","G","T","G"]},{Alleles:"G=0.62, A=0.38",Coord:"chr4:104052068",RS:"rs7661201",Haplotypes:["G","A","A","A","A","G"]},{Alleles:"G=0.968, A=0.032",Coord:"chr4:104055722",RS:"rs2623063",Haplotypes:["G","G","G","G","G","A"]},{Alleles:"C=0.968, T=0.032",Coord:"chr4:104057121",RS:"rs2623062",Haplotypes:["C","C","C","C","C","T"]},{Alleles:"G=0.968, A=0.032",Coord:"chr4:104057248",RS:"rs2720463",Haplotypes:["G","G","G","G","G","A"]},{Alleles:"T=0.968, G=0.032",Coord:"chr4:104057887",RS:"rs2711901",Haplotypes:["T","T","T","T","T","G"]},{Alleles:"T=0.968, C=0.032",Coord:"chr4:104051132",RS:"rs2623082",Haplotypes:["T","T","T","T","T","C"]},{Alleles:"G=0.968, A=0.032",Coord:"chr4:104058596",RS:"rs2711900",Haplotypes:["G","G","G","G","G","A"]},{Alleles:"G=0.968, A=0.032",Coord:"chr4:104050510",RS:"rs2720456",Haplotypes:["G","G","G","G","G","A"]},{Alleles:"G=0.968, A=0.032",Coord:"chr4:104050326",RS:"rs2720455",Haplotypes:["G","G","G","G","G","A"]},{Alleles:"G=1.0, A=0.0",Coord:"chr4:104059542",RS:"rs2243682",Haplotypes:["G","G","G","G","G","G"]}]};
-var ldassocData=[{RS_Number:"rs75563749",Coord:"chr3:171031233",Alleles:"(A/T)",MAF:.1983,Distance:348304,Dprime:.0512,R2:.0021,Correlated_Alleles:"= , =",FORGEdb:10,RegulomeDB:6,Functional_Class:"NA"},{RS_Number:"rs76189435",Coord:"chr3:170980080",Alleles:"(C/G)",MAF:.0527,Distance:-51153,Dprime:.622,R2:.0871,Correlated_Alleles:"= , =",FORGEdb:10,RegulomeDB:"2b",Functional_Class:"NA"},{RS_Number:"rs76140932",Coord:"chr3:170980434",Alleles:"(A/G)",MAF:.0539,Distance:-50799,Dprime:.6073,R2:.085,Correlated_Alleles:"= , =",FORGEdb:10,RegulomeDB:"2b",Functional_Class:"NA"},{RS_Number:"rs76735261",Coord:"chr3:170981252",Alleles:"(G/C)",MAF:.0539,Distance:-49981,Dprime:.6073,R2:.085,Correlated_Alleles:"= , =",FORGEdb:8,RegulomeDB:5,Functional_Class:"NA"},{RS_Number:"rs1158564",Coord:"chr3:171002654",Alleles:"(A/G)",MAF:.4439,Distance:-28579,Dprime:.866,R2:.2324,Correlated_Alleles:"A=A,G=T",FORGEdb:7,RegulomeDB:"2b",Functional_Class:"NA"},{RS_Number:"rs4894756",Coord:"chr3:171002036",Alleles:"(G/A)",MAF:.3806,Distance:-29197,Dprime:.8732,R2:.3069,Correlated_Alleles:"G=A,A=T",FORGEdb:7,RegulomeDB:4,Functional_Class:"NA"},{RS_Number:"rs200296423",Coord:"chr3:170969849",Alleles:"(TGCG/-)",MAF:.0475,Distance:-61384,Dprime:.5965,R2:.0718,Correlated_Alleles:"= , =",FORGEdb:"",RegulomeDB:".",Functional_Class:"NA"},{RS_Number:"rs377580557",Coord:"chr3:171001114",Alleles:"(TTTTCTC/-)",MAF:.0445,Distance:-30119,Dprime:.67,R2:.0846,Correlated_Alleles:"= , =",FORGEdb:"",RegulomeDB:".",Functional_Class:"NA"},{RS_Number:"rs377580557",Coord:"chr3:171001114",Alleles:"(TTTTCTC/-)",MAF:.0445,Distance:-30119,Dprime:.67,R2:.0846,Correlated_Alleles:"= , =",FORGEdb:"",RegulomeDB:".",Functional_Class:"NA"},{RS_Number:"rs6444976",Coord:"chr3:171002143",Alleles:"(G/C)",MAF:.3808,Distance:-29090,Dprime:.8731,R2:.3066,Correlated_Alleles:"G=A,C=T",FORGEdb:6,RegulomeDB:4,Functional_Class:"NA"},{RS_Number:"rs13090306",Coord:"chr3:170969666",Alleles:"(A/C)",MAF:.4163,Distance:-61567,Dprime:.5359,R2:.0996,Correlated_Alleles:"= , =",FORGEdb:9,RegulomeDB:5,Functional_Class:"NA"}];
-var snpclipData = {"warnings":[{"rs_number":"rs12980602","position":"chr19:39752820","alleles":"T=0.763, C=0.237","comment":"SNP kept","rs_number_link":"<a>rs12980602</a>","position_link":"<a>chr19:39752820</a>"},{"rs_number":"rs35963157","position":"chr19:39745695","alleles":"-=0.338, C=0.662","comment":"SNP in LD with rs11322783 (R2=0.1887), SNP removed","rs_number_link":"<a>rs35963157</a>","position_link":"<a>chr19:39745695</a>"}],"details":[{"rs_number":"rs12980602","position":"chr19:39752820","alleles":"T=0.763, C=0.237","comment":"SNP kept","rs_number_link":"<a>rs12980602</a>","position_link":"<a>chr19:39752820</a>"},{"rs_number":"rs35963157","position":"chr19:39745695","alleles":"-=0.338, C=0.662","comment":"SNP in LD with rs11322783 (R2=0.1887), SNP removed","rs_number_link":"<a>rs35963157</a>","position_link":"<a>chr19:39745695</a>"}]};
-var snpchipData = {"snpchip":[{"rs_number":"<a href=\"http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=505066\" target=\"rs_number_rs505066\">rs505066</a>","chromosome":"1","position":"<a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A96882421-96882921&snp142=pack&hgFind.matches=rs505066\" target=\"coord_chr1:96882671\">96882671</a>","map":["&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X","X","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;"]},{"rs_number":"<a href=\"http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4478775\" target=\"rs_number_rs4478775\">rs4478775</a>","chromosome":"1","position":"<a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A177769847-177770347&snp142=pack&hgFind.matches=rs4478775\" target=\"coord_chr1:177770097\">177770097</a>","map":["&nbsp;","X","&nbsp;","X","&nbsp;","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X","X","X","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X"]},{"rs_number":"<a href=\"http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=561634\" target=\"rs_number_rs561634\">rs561634</a>","chromosome":"1","position":"<a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A177895513-177896013&snp142=pack&hgFind.matches=rs561634\" target=\"coord_chr1:177895763\">177895763</a>","map":["&nbsp;","X","&nbsp;","X","&nbsp;","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X","X","X","X","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","&nbsp;","X"]},{"rs_number":"<a href=\"http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2820292\" target=\"rs_number_rs2820292\">rs2820292</a>","chromosome":"1","position":"<a href=\"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A201784037-201784537&snp142=pack&hgFind.matches=rs2820292\" target=\"coord_chr1:201784287\">201784287</a>","map":["X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X"]}],"headers":[{"code":"A_AFR","platform":"Affymetrix Axiom GW AFR"},{"code":"A_ASI","platform":"Affymetrix Axiom GW ASI"},{"code":"A_EAS","platform":"Affymetrix Axiom GW EAS"},{"code":"A_EUR","platform":"Affymetrix Axiom GW EUR"},{"code":"A_Hu","platform":"Affymetrix Axiom GW Hu"},{"code":"A_Hu-CHB","platform":"Affymetrix Axiom GW Hu-CHB"},{"code":"A_LAT","platform":"Affymetrix Axiom GW LAT"},{"code":"A_Onco","platform":"Affymetrix OncoScan"},{"code":"A_OncoCNV","platform":"Affymetrix OncoScan CNV"},{"code":"A_SNP6.0","platform":"Affymetrix SNP 6.0"},{"code":"I_CardioMetab","platform":"Illumina Cardio-MetaboChip"},{"code":"I_1M-D","platform":"Illumina Human1M-Duov3"},{"code":"I_1M","platform":"Illumina Human1Mv1"},{"code":"I_Exon510S","platform":"Illumina HumanExon510Sv1"},{"code":"I_O1S-8","platform":"Illumina HumanOmni1S-8v1"},{"code":"I_O2.5-4","platform":"Illumina HumanOmni2.5-4v1"},{"code":"I_O2.5-8","platform":"Illumina HumanOmni2.5-8v1.2"},{"code":"I_O2.5E-8v1","platform":"Illumina HumanOmni2.5Exome-8v1"},{"code":"I_O2.5E-8v1.1","platform":"Illumina HumanOmni2.5Exome-8v1.1"},{"code":"I_O2.5E-8v1.2","platform":"Illumina HumanOmni2.5Exome-8v1.2"},{"code":"I_O5-4","platform":"Illumina HumanOmni5-4v1"},{"code":"I_O5E-4","platform":"Illumina HumanOmni5Exome-4v1"},{"code":"I_ME-Global-8","platform":"Illumina Infinium Multi-Ethnic Global-8"}]};
+var restService = {
+	protocol: window.location.protocol,
+	hostname: window.location.host,
+	pathname: window.location.pathname,
+	route: 'LDlinkRestWeb',
+};
+var restServerUrl =
+	restService.protocol +
+	'//' +
+	restService.hostname +
+	restService.pathname +
+	restService.route;
+
+var dropdowns = ['assoc-chromosome', 'assoc-position', 'assoc-p-value'];
+
+var populations = {
+	AFR: {
+		fullName: 'African',
+		subPopulations: {
+			YRI: 'Yoruba in Ibadan, Nigera',
+			LWK: ' Luhya in Webuye, Kenya',
+			GWD: ' Gambian in Western Gambia',
+			MSL: '  Mende in Sierra Leone',
+			ESN: '  Esan in Nigera',
+			ASW: ' Americans of African Ancestry in SW USA',
+			ACB: '  African Carribbeans in Barbados',
+		},
+	},
+	AMR: {
+		fullName: 'Ad Mixed American',
+		subPopulations: {
+			MXL: '  Mexican Ancestry from Los Angeles, USA',
+			PUR: ' Puerto Ricans from Puerto Rico',
+			CLM: ' Colombians from Medellin, Colombia',
+			PEL: ' Peruvians from Lima, Peru',
+		},
+	},
+	EAS: {
+		fullName: 'East Asian',
+		subPopulations: {
+			CHB: ' Han Chinese in Bejing, China',
+			JPT: ' Japanese in Tokyo, Japan',
+			CHS: ' Southern Han Chinese',
+			CDX: ' Chinese Dai in Xishuangbanna, China',
+			KHV: '  Kinh in Ho Chi Minh City, Vietnam',
+		},
+	},
+	EUR: {
+		fullName: 'European',
+		subPopulations: {
+			CEU: ' Utah Residents from North and West Europe',
+			TSI: '  Toscani in Italia',
+			FIN: '  Finnish in Finland',
+			GBR: ' British in England and Scotland',
+			IBS: '  Iberian population in Spain',
+		},
+	},
+	SAS: {
+		fullName: 'South Asian',
+		subPopulations: {
+			GIH: '  Gujarati Indian from Houston, Texas',
+			PJL: '  Punjabi from Lahore, Pakistan',
+			BEB: '  Bengali from Bangladesh',
+			STU: '  Sri Lankan Tamil from the UK',
+			ITU: ' Indian Telugu from the UK',
+		},
+	},
+};
+var ldPairData = {
+	corr_alleles: [
+		'rs2720460(A) allele is correlated with rs11733615(C) allele',
+		'rs2720460(G) allele is correlated with rs11733615(T) allele',
+	],
+	haplotypes: {
+		hap1: { alleles: 'AC', count: '155', frequency: '0.686' },
+		hap2: { alleles: 'GC', count: '40', frequency: '0.177' },
+		hap3: { alleles: 'GT', count: '29', frequency: '0.128' },
+		hap4: { alleles: 'AT', count: '2', frequency: '0.009' },
+	},
+	snp1: {
+		allele_1: { allele: 'A', count: '157', frequency: '0.695' },
+		allele_2: { allele: 'G', count: '69', frequency: '0.305' },
+		coord: 'chr4:104054686',
+		rsnum: 'rs2720460',
+	},
+	snp2: {
+		allele_1: { allele: 'C', count: '195', frequency: '0.863' },
+		allele_2: { allele: 'T', count: '31', frequency: '0.137' },
+		coord: 'chr4:104157164',
+		rsnum: 'rs11733615',
+	},
+	statistics: { chisq: '67.271', d_prime: '0.9071', p: '0.0', r2: '0.2977' },
+	two_by_two: {
+		cells: { c11: '155', c12: '2', c21: '40', c22: '29' },
+		total: 'old - 227',
+	},
+};
+var ldhapData = {
+	footer: [
+		{ Count: 127, Frequency: 0.588, Haplotype: 'GCATGGCGTTGGGG' },
+		{ Count: 40, Frequency: 0.1852, Haplotype: 'GGGGAGCGTTGGGG' },
+		{ Count: 23, Frequency: 0.1065, Haplotype: 'GCGGAGCGTTGGGG' },
+		{ Count: 11, Frequency: 0.0509, Haplotype: 'TGGGAGCGTTGGGG' },
+		{ Count: 8, Frequency: 0.037, Haplotype: 'GCATAGCGTTGGGG' },
+		{ Count: 7, Frequency: 0.0324, Haplotype: 'TGGGGATAGCAAAG' },
+	],
+	rows: [
+		{
+			Alleles: 'G=0.917, T=0.083',
+			Coord: 'chr4:104050980',
+			RS: 'rs2720457',
+			Haplotypes: ['G', 'G', 'G', 'T', 'G', 'T'],
+		},
+		{
+			Alleles: 'C=0.732, G=0.269',
+			Coord: 'chr4:104052963',
+			RS: 'rs2720458',
+			Haplotypes: ['C', 'G', 'C', 'G', 'C', 'G'],
+		},
+		{
+			Alleles: 'A=0.625, G=0.375',
+			Coord: 'chr4:104055748',
+			RS: 'rs2720461',
+			Haplotypes: ['A', 'G', 'G', 'G', 'A', 'G'],
+		},
+		{
+			Alleles: 'T=0.625, G=0.375',
+			Coord: 'chr4:104056210',
+			RS: 'rs2720462',
+			Haplotypes: ['T', 'G', 'G', 'G', 'T', 'G'],
+		},
+		{
+			Alleles: 'G=0.62, A=0.38',
+			Coord: 'chr4:104052068',
+			RS: 'rs7661201',
+			Haplotypes: ['G', 'A', 'A', 'A', 'A', 'G'],
+		},
+		{
+			Alleles: 'G=0.968, A=0.032',
+			Coord: 'chr4:104055722',
+			RS: 'rs2623063',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'A'],
+		},
+		{
+			Alleles: 'C=0.968, T=0.032',
+			Coord: 'chr4:104057121',
+			RS: 'rs2623062',
+			Haplotypes: ['C', 'C', 'C', 'C', 'C', 'T'],
+		},
+		{
+			Alleles: 'G=0.968, A=0.032',
+			Coord: 'chr4:104057248',
+			RS: 'rs2720463',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'A'],
+		},
+		{
+			Alleles: 'T=0.968, G=0.032',
+			Coord: 'chr4:104057887',
+			RS: 'rs2711901',
+			Haplotypes: ['T', 'T', 'T', 'T', 'T', 'G'],
+		},
+		{
+			Alleles: 'T=0.968, C=0.032',
+			Coord: 'chr4:104051132',
+			RS: 'rs2623082',
+			Haplotypes: ['T', 'T', 'T', 'T', 'T', 'C'],
+		},
+		{
+			Alleles: 'G=0.968, A=0.032',
+			Coord: 'chr4:104058596',
+			RS: 'rs2711900',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'A'],
+		},
+		{
+			Alleles: 'G=0.968, A=0.032',
+			Coord: 'chr4:104050510',
+			RS: 'rs2720456',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'A'],
+		},
+		{
+			Alleles: 'G=0.968, A=0.032',
+			Coord: 'chr4:104050326',
+			RS: 'rs2720455',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'A'],
+		},
+		{
+			Alleles: 'G=1.0, A=0.0',
+			Coord: 'chr4:104059542',
+			RS: 'rs2243682',
+			Haplotypes: ['G', 'G', 'G', 'G', 'G', 'G'],
+		},
+	],
+};
+var ldassocData = [
+	{
+		RS_Number: 'rs75563749',
+		Coord: 'chr3:171031233',
+		Alleles: '(A/T)',
+		MAF: 0.1983,
+		Distance: 348304,
+		Dprime: 0.0512,
+		R2: 0.0021,
+		Correlated_Alleles: '= , =',
+		FORGEdb: 10,
+		RegulomeDB: 6,
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs76189435',
+		Coord: 'chr3:170980080',
+		Alleles: '(C/G)',
+		MAF: 0.0527,
+		Distance: -51153,
+		Dprime: 0.622,
+		R2: 0.0871,
+		Correlated_Alleles: '= , =',
+		FORGEdb: 10,
+		RegulomeDB: '2b',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs76140932',
+		Coord: 'chr3:170980434',
+		Alleles: '(A/G)',
+		MAF: 0.0539,
+		Distance: -50799,
+		Dprime: 0.6073,
+		R2: 0.085,
+		Correlated_Alleles: '= , =',
+		FORGEdb: 10,
+		RegulomeDB: '2b',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs76735261',
+		Coord: 'chr3:170981252',
+		Alleles: '(G/C)',
+		MAF: 0.0539,
+		Distance: -49981,
+		Dprime: 0.6073,
+		R2: 0.085,
+		Correlated_Alleles: '= , =',
+		FORGEdb: 8,
+		RegulomeDB: 5,
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs1158564',
+		Coord: 'chr3:171002654',
+		Alleles: '(A/G)',
+		MAF: 0.4439,
+		Distance: -28579,
+		Dprime: 0.866,
+		R2: 0.2324,
+		Correlated_Alleles: 'A=A,G=T',
+		FORGEdb: 7,
+		RegulomeDB: '2b',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs4894756',
+		Coord: 'chr3:171002036',
+		Alleles: '(G/A)',
+		MAF: 0.3806,
+		Distance: -29197,
+		Dprime: 0.8732,
+		R2: 0.3069,
+		Correlated_Alleles: 'G=A,A=T',
+		FORGEdb: 7,
+		RegulomeDB: 4,
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs200296423',
+		Coord: 'chr3:170969849',
+		Alleles: '(TGCG/-)',
+		MAF: 0.0475,
+		Distance: -61384,
+		Dprime: 0.5965,
+		R2: 0.0718,
+		Correlated_Alleles: '= , =',
+		FORGEdb: '',
+		RegulomeDB: '.',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs377580557',
+		Coord: 'chr3:171001114',
+		Alleles: '(TTTTCTC/-)',
+		MAF: 0.0445,
+		Distance: -30119,
+		Dprime: 0.67,
+		R2: 0.0846,
+		Correlated_Alleles: '= , =',
+		FORGEdb: '',
+		RegulomeDB: '.',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs377580557',
+		Coord: 'chr3:171001114',
+		Alleles: '(TTTTCTC/-)',
+		MAF: 0.0445,
+		Distance: -30119,
+		Dprime: 0.67,
+		R2: 0.0846,
+		Correlated_Alleles: '= , =',
+		FORGEdb: '',
+		RegulomeDB: '.',
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs6444976',
+		Coord: 'chr3:171002143',
+		Alleles: '(G/C)',
+		MAF: 0.3808,
+		Distance: -29090,
+		Dprime: 0.8731,
+		R2: 0.3066,
+		Correlated_Alleles: 'G=A,C=T',
+		FORGEdb: 6,
+		RegulomeDB: 4,
+		Functional_Class: 'NA',
+	},
+	{
+		RS_Number: 'rs13090306',
+		Coord: 'chr3:170969666',
+		Alleles: '(A/C)',
+		MAF: 0.4163,
+		Distance: -61567,
+		Dprime: 0.5359,
+		R2: 0.0996,
+		Correlated_Alleles: '= , =',
+		FORGEdb: 9,
+		RegulomeDB: 5,
+		Functional_Class: 'NA',
+	},
+];
+var snpclipData = {
+	warnings: [
+		{
+			rs_number: 'rs12980602',
+			position: 'chr19:39752820',
+			alleles: 'T=0.763, C=0.237',
+			comment: 'SNP kept',
+			rs_number_link: '<a>rs12980602</a>',
+			position_link: '<a>chr19:39752820</a>',
+		},
+		{
+			rs_number: 'rs35963157',
+			position: 'chr19:39745695',
+			alleles: '-=0.338, C=0.662',
+			comment: 'SNP in LD with rs11322783 (R2=0.1887), SNP removed',
+			rs_number_link: '<a>rs35963157</a>',
+			position_link: '<a>chr19:39745695</a>',
+		},
+	],
+	details: [
+		{
+			rs_number: 'rs12980602',
+			position: 'chr19:39752820',
+			alleles: 'T=0.763, C=0.237',
+			comment: 'SNP kept',
+			rs_number_link: '<a>rs12980602</a>',
+			position_link: '<a>chr19:39752820</a>',
+		},
+		{
+			rs_number: 'rs35963157',
+			position: 'chr19:39745695',
+			alleles: '-=0.338, C=0.662',
+			comment: 'SNP in LD with rs11322783 (R2=0.1887), SNP removed',
+			rs_number_link: '<a>rs35963157</a>',
+			position_link: '<a>chr19:39745695</a>',
+		},
+	],
+};
+var snpchipData = {
+	snpchip: [
+		{
+			rs_number:
+				'<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=505066" target="rs_number_rs505066">rs505066</a>',
+			chromosome: '1',
+			position:
+				'<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A96882421-96882921&snp142=pack&hgFind.matches=rs505066" target="coord_chr1:96882671">96882671</a>',
+			map: [
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+				'X',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+			],
+		},
+		{
+			rs_number:
+				'<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4478775" target="rs_number_rs4478775">rs4478775</a>',
+			chromosome: '1',
+			position:
+				'<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A177769847-177770347&snp142=pack&hgFind.matches=rs4478775" target="coord_chr1:177770097">177770097</a>',
+			map: [
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+				'X',
+				'X',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+			],
+		},
+		{
+			rs_number:
+				'<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=561634" target="rs_number_rs561634">rs561634</a>',
+			chromosome: '1',
+			position:
+				'<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A177895513-177896013&snp142=pack&hgFind.matches=rs561634" target="coord_chr1:177895763">177895763</a>',
+			map: [
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+				'X',
+				'X',
+				'X',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'&nbsp;',
+				'X',
+			],
+		},
+		{
+			rs_number:
+				'<a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2820292" target="rs_number_rs2820292">rs2820292</a>',
+			chromosome: '1',
+			position:
+				'<a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A201784037-201784537&snp142=pack&hgFind.matches=rs2820292" target="coord_chr1:201784287">201784287</a>',
+			map: [
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+				'X',
+			],
+		},
+	],
+	headers: [
+		{ code: 'A_AFR', platform: 'Affymetrix Axiom GW AFR' },
+		{ code: 'A_ASI', platform: 'Affymetrix Axiom GW ASI' },
+		{ code: 'A_EAS', platform: 'Affymetrix Axiom GW EAS' },
+		{ code: 'A_EUR', platform: 'Affymetrix Axiom GW EUR' },
+		{ code: 'A_Hu', platform: 'Affymetrix Axiom GW Hu' },
+		{ code: 'A_Hu-CHB', platform: 'Affymetrix Axiom GW Hu-CHB' },
+		{ code: 'A_LAT', platform: 'Affymetrix Axiom GW LAT' },
+		{ code: 'A_Onco', platform: 'Affymetrix OncoScan' },
+		{ code: 'A_OncoCNV', platform: 'Affymetrix OncoScan CNV' },
+		{ code: 'A_SNP6.0', platform: 'Affymetrix SNP 6.0' },
+		{ code: 'I_CardioMetab', platform: 'Illumina Cardio-MetaboChip' },
+		{ code: 'I_1M-D', platform: 'Illumina Human1M-Duov3' },
+		{ code: 'I_1M', platform: 'Illumina Human1Mv1' },
+		{ code: 'I_Exon510S', platform: 'Illumina HumanExon510Sv1' },
+		{ code: 'I_O1S-8', platform: 'Illumina HumanOmni1S-8v1' },
+		{ code: 'I_O2.5-4', platform: 'Illumina HumanOmni2.5-4v1' },
+		{ code: 'I_O2.5-8', platform: 'Illumina HumanOmni2.5-8v1.2' },
+		{ code: 'I_O2.5E-8v1', platform: 'Illumina HumanOmni2.5Exome-8v1' },
+		{ code: 'I_O2.5E-8v1.1', platform: 'Illumina HumanOmni2.5Exome-8v1.1' },
+		{ code: 'I_O2.5E-8v1.2', platform: 'Illumina HumanOmni2.5Exome-8v1.2' },
+		{ code: 'I_O5-4', platform: 'Illumina HumanOmni5-4v1' },
+		{ code: 'I_O5E-4', platform: 'Illumina HumanOmni5Exome-4v1' },
+		{
+			code: 'I_ME-Global-8',
+			platform: 'Illumina Infinium Multi-Ethnic Global-8',
+		},
+	],
+};
 var snpchipReverseLookup = [];
 var ldExpressRaw;
 var ldExpressSort;
@@ -21,1391 +545,1615 @@ var ldTraitRaw;
 var ldTraitSort;
 var ldClipRaw;
 var tissueJSON;
-var modules = [ "ldassoc", "ldexpress", "ldhap", "ldmatrix", "ldpair", "ldpop", "ldproxy", "ldtrait", "snpclip", "snpchip", "apiaccess" ];
-var headerModules = [ "ldassoc", "ldexpress", "ldhap", "ldmatrix", "ldpair", "ldpop", "ldproxy", "ldtrait", "snpclip", "snpchip" ];
+var modules = [
+	'ldassoc',
+	'ldexpress',
+	'ldhap',
+	'ldmatrix',
+	'ldpair',
+	'ldpop',
+	'ldproxy',
+	'ldtrait',
+	'snpclip',
+	'snpchip',
+	'apiaccess',
+];
+var headerModules = [
+	'ldassoc',
+	'ldexpress',
+	'ldhap',
+	'ldmatrix',
+	'ldpair',
+	'ldpop',
+	'ldproxy',
+	'ldtrait',
+	'snpclip',
+	'snpchip',
+];
 var homeStartBox = 0;
 var newsList = [];
 var moduleTitleDescription = {
-    "ldassoc": ["LDassoc Tool", "#LDassoc", "Interactively visualize association p-value results and linkage disequilibrium patterns for a genomic region of interest."],
-    "ldexpress": ["LDexpress Tool", "#LDexpress", "Search if a list of variants (or variants in LD with those variants) is associated with gene expression in multiple tissue types."],
-    "ldhap": ["LDhap Tool", "#LDhap", "Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants."],
-    "ldmatrix": ["LDmatrix Tool", "#LDmatrix", "Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics."],
-    "ldpair": ["LDpair Tool", "#LDpair", "Investigate correlated alleles for a pair of variants in high LD."],
-    "ldpop": ["LDpop Tool", "#LDpop", "Investigate allele frequencies and linkage disequilibrium patterns across 1000G populations."],
-    "ldproxy": ["LDproxy Tool", "#LDproxy", "Interactively explore proxy and putatively functional variants for a query variant."],
-    "ldtrait": ["LDtrait Tool", "#LDtrait", "Search if a list of variants (or variants in LD with those variants) have previously been associated with a trait or disease."],
-    "snpclip": ["SNPclip Tool", "#SNPclip", "Prune a list of variants by linkage disequilibrium."],
-    "snpchip": ["SNPchip Tool", "#SNPchip", "Find commercial genotyping platforms for variants."],
-    "apiaccess": ["API Access", "#APIaccess", "LDlink modules are also accessible via command line from a terminal. This programmatic access facilitates researchers who are \
+	ldassoc: [
+		'LDassoc Tool',
+		'#LDassoc',
+		'Interactively visualize association p-value results and linkage disequilibrium patterns for a genomic region of interest.',
+	],
+	ldexpress: [
+		'LDexpress Tool',
+		'#LDexpress',
+		'Search if a list of variants (or variants in LD with those variants) is associated with gene expression in multiple tissue types.',
+	],
+	ldhap: [
+		'LDhap Tool',
+		'#LDhap',
+		'Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants.',
+	],
+	ldmatrix: [
+		'LDmatrix Tool',
+		'#LDmatrix',
+		'Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics.',
+	],
+	ldpair: [
+		'LDpair Tool',
+		'#LDpair',
+		'Investigate correlated alleles for a pair of variants in high LD.',
+	],
+	ldpop: [
+		'LDpop Tool',
+		'#LDpop',
+		'Investigate allele frequencies and linkage disequilibrium patterns across 1000G populations.',
+	],
+	ldproxy: [
+		'LDproxy Tool',
+		'#LDproxy',
+		'Interactively explore proxy and putatively functional variants for a query variant.',
+	],
+	ldtrait: [
+		'LDtrait Tool',
+		'#LDtrait',
+		'Search if a list of variants (or variants in LD with those variants) have previously been associated with a trait or disease.',
+	],
+	snpclip: [
+		'SNPclip Tool',
+		'#SNPclip',
+		'Prune a list of variants by linkage disequilibrium.',
+	],
+	snpchip: [
+		'SNPchip Tool',
+		'#SNPchip',
+		'Find commercial genotyping platforms for variants.',
+	],
+	apiaccess: [
+		'API Access',
+		'#APIaccess',
+		'LDlink modules are also accessible via command line from a terminal. This programmatic access facilitates researchers who are \
     interested in performing batch queries. The syntax is similar to the web address link created for queries on the webpage. Generally text output \
     is returned that is the same as the file a user would download from the online site. Please register below for an access token required for your \
     API call. Once registered, your access token will be emailed to you.Interactively visualize association p-value results and linkage disequilibrium \
-    patterns for a genomic region of interest."]
+    patterns for a genomic region of interest.',
+	],
 };
 try {
-    const urlParams = new URLSearchParams(window.location.search);
-    var genomeBuild = urlParams.get('genome_build') ? urlParams.get('genome_build') : 'grch37';
+	const urlParams = new URLSearchParams(window.location.search);
+	var genomeBuild = urlParams.get('genome_build')
+		? urlParams.get('genome_build')
+		: 'grch37';
 } catch {
-    var genomeBuild = "grch37";
+	var genomeBuild = 'grch37';
 }
 
-
-Object.size = function(obj) {
-    var size = 0, key;
-    for (key in obj) {
-        if (obj.hasOwnProperty(key)) size++;
-    }
-    return size;
+Object.size = function (obj) {
+	var size = 0,
+		key;
+	for (key in obj) {
+		if (obj.hasOwnProperty(key)) size++;
+	}
+	return size;
 };
 
-
-$(document).ready(function() {
-
-    // Close URL change alert banner after 5 seconds
-    $("#url-alert").delay(5000).slideUp(600, function() {
-        $(this).alert('close');
-    });
-
-    // Load news text from news.html to news-container div
-    $.get("news.html?v=5.6.0", function (data) {
-        let tmpData = data.split("<p>")
-        let i = 0;
-        var newsHTMLList = [];
-        
-        for (i = 1; i < tmpData.length; i++){
-            let toPush = "<p>" + tmpData[i];
-            newsHTMLList.push(toPush);
-        }
-
-        let lastNews = "";
-        let versionNews=newsHTMLList[0].replace("<br>","");
-        let numFound = 0;
-        for(let i = 0; i < 1; i++){
-            if(versionNews.indexOf("</li>") != -1){
-                lastNews += versionNews.substring(0, versionNews.indexOf("</li>") + 5);
-                versionNews = versionNews.substring(versionNews.indexOf("</li>") + 6);
-                numFound += 1;
-            }
-            else{
-                i = 1;
-            }
-        }
-        if(versionNews.indexOf("</li>") != -1){
-            lastNews += "</ul> <a class=\"version-link\">Show more...</a>"
-        }
-        lastNews = lastNews.substring(0, lastNews.indexOf("<ul>") + 3) + " style=\"padding-left:10px; margin-bottom:0;\"" + lastNews.substring(lastNews.indexOf("<ul>") + 3);
-        // console.log(lastNews);
-        
-        newsList.push(lastNews + "<p style=\"margin-bottom:0px; margin-top:5px;\">(See <a class=\"version-link\">Version History</a>)</p>");
-        newsList.push("<p><b>LDlinkR</b><br></p><div style=\"height:4px;\"/><p style=\"margin:0;\">Interested in accessing LDlink's API using R? <br style=\"margin-bottom:5px;\">Check out the new LDlinkR package now available on <a href=\"https://cran.r-project.org/web/packages/LDlinkR/index.html\" title=\"LDlinkR CRAN\" target=\"_blank\">CRAN</a>.</p>")
-        newsList.push("<p><b>GWAS Explorer</b><br></p><div style=\"height:4px;\"/><p>Visualize and interact with genome-wide association study results from PLCO Atlas.</b> <br style=\"margin-bottom:5px;\">Check out <a href=\"https://exploregwas.cancer.gov/plco-atlas/\" title=\"GWAS Explorer\" target=\"_blank\">GWAS Explorer</a>. </p>")
-        newsList.push("<p><b>AuthorArranger</b><br></p><div style=\"height:4px;\"/><p>Bogged down organizing authors and affiliations on journal title pages for large studies?</b> <br style=\"margin-bottom:5px;\">Check out <a href=\"https://authorarranger.nih.gov/\" title=\"Author Arranger\" target=\"_blank\">AuthorArranger</a> and conquer title pages in seconds! </p>")
-
-        $("#news-card-1").html(newsList[0].replace("<br>",""));
-        $("#news-card-2").html(newsList[1]);
-        $("#news-card-3").html(newsList[2]);
-        // console.log(newsList)
-        testResize();
-        $(".version-link").on('click',function(){
-            $('#version-tab-anchor').click();
-            window.scrollTo(0,0);
-        });
-        $("#news-container").append(data);
-    });
-    
-    $('#progressbar').progressbar();
-    //$('#progressbar').progressbar('setPosition', 85);
-    //$('#ldassoc-progressbar').progressbar('reset');
-    $('#ldassoc-progressbar').on("positionChanged", function (e) {
-        console.log(e.position);
-        console.log(e.percent);
-    });
-
-    $(':file').change(function(){
-        var file = this.files[0];
-        var name = file.name;
-        var size = file.size;
-        var type = file.type;
-        //Your validation
-        console.dir(file);
-    });
-    $.each(dropdowns, function(i, id) {
-        $("#"+id+" > .dropdown-menu").on("click", "li a", function(){
-            createCookie(id, $(this).text(), 10);
-            setBootstrapSelector(id, $(this).text());
-        });
-    });
-    $("#assoc-region > .dropdown-menu li a").click(function(e){
-        $("#assoc-region > .btn:first-child").html($(this).text() + '&nbsp;<span class="caret"></span>');
-        $("#assoc-region > .btn:first-child").val($(this).text().toLowerCase());
-        $("#region-gene-container").hide();
-        $("#region-region-container").hide();
-        $("#region-variant-container").hide();
-        console.log(e.target.id);
-        switch($(this).text()) {
-            case "Gene":
-                $("#region-gene-name").val('');
-                // $("#region-gene-base-pair-window").val('');
-                $("#region-gene-index").val('');
-                $("#region-region-start-coord").val('');
-                $("#region-region-end-coord").val('');
-                $("#region-region-index").val('');
-                $("#region-variant-index").val('');
-                // $("#region-variant-base-pair-window").val('');
-                $("#region-gene-container").show();
-                break;
-            case "Region":
-                $("#region-gene-name").val('');
-                // $("#region-gene-base-pair-window").val('');
-                $("#region-gene-index").val('');
-                $("#region-region-start-coord").val('');
-                $("#region-region-end-coord").val('');
-                $("#region-region-index").val('');
-                $("#region-variant-index").val('');
-                // $("#region-variant-base-pair-window").val('');
-                $("#region-region-container").show();
-                break;
-            case "Variant":
-                $("#region-gene-name").val('');
-                // $("#region-gene-base-pair-window").val('');
-                $("#region-gene-index").val('');
-                $("#region-region-start-coord").val('');
-                $("#region-region-end-coord").val('');
-                $("#region-region-index").val('');
-                $("#region-variant-index").val('');
-                // $("#region-variant-base-pair-window").val('');
-                $("#region-variant-container").show();
-                break;
-        }
-    });
-
-    // init genome build selection
-    switch(genomeBuild) {
-        case "grch37":
-            $(document).ready(function() {
-                $("#genome-build > .dropdown-menu li a")[0].click();
-            });
-            break;
-        case "grch38":
-            $(document).ready(function() {
-                $("#genome-build > .dropdown-menu li a")[1].click();
-            });
-            break;
-        case "grch38_high_coverage":
-            $(document).ready(function() {
-                $("#genome-build > .dropdown-menu li a")[2].click();
-            });
-            break;
-        default:
-            $(document).ready(function() {
-                $("#genome-build > .dropdown-menu li a")[0].click();
-            });
-    }
-    
-    $("#genome-build > .dropdown-menu li a").click(function(e){
-        $("#genome-build > .btn:first-child").html($(this).text() + '&nbsp;<span class="caret"></span>');
-        $("#genome-build > .btn:first-child").val($(this).text().toLowerCase());
-        // console.log($(this).attr("value"));
-        genomeBuild = $(this).attr("value");
-        // change ldassoc example inputs
-        if (document.getElementById('example-gwas').checked) {
-            setupLDassocExample();
-        }
-    });
-
-    // Hide Genome Build dropdown on LD Tools dropdown-nav hover 
-    dropdownTools = document.querySelector("#dropdown-tools");
-    dropdownTools.addEventListener("mouseover", event => {
-        $("#genome-build").click()
-    });
-
-    $('#ldassoc').prop('disabled', true);
-
-    // reset apiaccess form
-    $(".apiaccess-done").click(function(e) {
-        $("#apiaccess-reset").click();
-        $("#apiaccess-new-user").modal('hide');
-        $("#apiaccess-existing-user").modal('hide');
-
-        $('#apiblocked-form').show();
-        $('#apiblocked').show();
-        $('#apiblocked-submit-message').hide();
-        $('#apiblocked-done').val("Cancel");
-
-        $("#apiblocked-reset").click();
-        $("#apiaccess-blocked-user").modal('hide');
-    });
-
-    $("#example-gwas").click(function(e){
-        setupLDassocExample();
-    });
-
-    updateVersion(ldlink_version);
-    //addValidators();
-    $('#ldlink-tabs').on('click', 'a', function(e) {
-        // console.warn("You clicked a tab");
-        
-        //console.info("Check for an attribute called data-url");
-        //If data-url use that.
-        var currentTab = e.target.id.substr(0, e.target.id.search('-'));
-        // console.log('currentTab: ' + currentTab)
-        clearTabs(currentTab);
-        //console.log(currentTab);
-        var last_url_params = $("#"+currentTab+"-tab-anchor").attr("data-url-params");
-        //console.log("last_url_params: "+last_url_params);
-        if(typeof last_url_params === "undefined") {
-            window.history.pushState({},'', "?tab="+currentTab);
-        } else {
-            window.history.pushState({},'', "?"+last_url_params);
-        }
-
-        
-    });
-    
-    setupLDexpressControls();
-    setupLDtraitControls();
-    setupSNPclipControls();
-    setupSNPchipControls();
-    showFFWarning();
-
-    createAssocTable();
-    createPopTable();
-    createProxyTable();
-    createExpressDetailsTable();
-    createExpressQueryWarningsTable();
-    createTraitDetailsTable();
-    createTraitQueryWarningsTable();
-    var new_assoc_data = {
-        "aaData": [
-            ["rs75563749","chr7","24958977","(C/T)","0.2037",-726,"0.234","0.234","C-C","0.0", "10","7","HaploReg link","NA"],
-            ["rs95696732","chr4","24958977","(C/T)","0.2037",-726,"1.0","1.0","T-T","0.0","","7","HaploReg link","NA"]
-        ]
-    };
-
-    var new_proxy_data = {
-        "aaData": [
-            ["rs125","chr7","24958977","(C/T)","0.2037",-726,"1.0","1.0","C-C,T-T","8","7","HaploReg link","NA"],
-            ["rs128","chr7","24958977","(C/T)","0.2037",-726,"1.0","1.0","C-C,T-T","9","7","HaploReg link","NA"],
-            [".","chr4","24958977","(C/T)","0.2037",-726,"1.0","1.0","C-C,T-T","9","7","HaploReg link","NA"]
-        ]
-    };
-
-    // var new_trait_data = {
-    //     "aaData": [
-    //         ["cognitive function measurement","rs77052120","chr1:110765398","Variant found in GWAS catalog within window."],
-    //     ]
-    // };
-    
-    RefreshTable('#new-ldassoc', new_assoc_data);
-    RefreshTable('#new-ldproxy', new_proxy_data);
-
-    $('[data-toggle="popover"]').popover();
-
-    loadHelp();
-
-    // Apply Bindings
-    ko.applyBindings(ldpairModel, document
-            .getElementById('ldpair-results-container'));
-    ko.applyBindings(ldhapModel, document
-            .getElementById('ldhap-results-container'));
-    ko.applyBindings(snpclipModel, document
-            .getElementById('snpclip-results-container'));
-    ko.applyBindings(snpchipModel, document
-            .getElementById('snpchip-results-container'));
-
-    $.each(modules, function(key, id) {
-        buildPopulationDropdown(id + "-population-codes");
-        $("#"+ id + "-results-container").hide();
-        $('#'+ id + '-message').hide();
-        $('#'+ id + '-message-warning').hide();
-        $('#'+ id + "-loading").hide();
-    });
-    
-    $('#apiblocked-loading').hide();
-    $('#apiblocked-message').hide();
-    $('#apiblocked-message-warning').hide();
-
-    $('.ldlinkForm').on('submit', function(e) {
-        calculate(e);
-    });
-
-    $(".help-anchor-link").on('click', function(e) { 
-        var tab = e.target.hash;
-        $('#help-tab-anchor').click();
-        setTimeout(function() {
-            window.location = tab;
-        }, 500);
-        window.scrollTo(0,0);
-    });
-
-    $(".anchor-link").on('click', function(e) {
-        var tab = $(this).attr('dest');
-        $('#' + tab + '-tab-anchor').click();
-        window.scrollTo(0,0);
-    });
-
-    setupTabs();
-
-    autoCalculate();
-    createFileSelectEvent();
-    createEnterEvent();
-    initAPIExamples();
-    // Google Maps API
-    initMap();
-    // export LDpop map dropdown buttons
-    $("#ldpop-LD-downloadPNG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop LD map export png");
-        exportMap(1, "LD", "png");
-    });
-    $("#ldpop-LD-downloadJPEG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop LD export jpeg");
-        exportMap(1, "LD", "jpeg");
-    });
-    // export variant 1 allele freq map
-    $("#ldpop-AFvar1-downloadPNG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop variant 1 allele freq map export png");
-        exportMap(2, "AF", "png");
-    });
-    $("#ldpop-AFvar1-downloadJPEG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop variant 1 allele freq map export jpeg");
-        exportMap(2, "AF", "jpeg");
-    });
-    // export variant 2 allele freq map
-    $("#ldpop-AFvar2-downloadPNG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop variant 2 allele freq map export png");
-        exportMap(3, "AF", "png");
-    });
-    $("#ldpop-AFvar2-downloadJPEG").click(function(e) {
-        e.preventDefault();
-        // console.log("ldpop variant 2 allele freq map export jpeg");
-        exportMap(3, "AF", "jpeg");
-    });
-
-    // LDexpress change R2/D' threshold label
-    $("#ldexpress_ld_r2").click(function(e){
-        // console.log("R2");
-        $("#ldexpress_r2_d_threshold_label").html("R<sup>2</sup> &ge;");
-    });
-    $("#ldexpress_ld_d").click(function(e){
-        // console.log("D");
-        $("#ldexpress_r2_d_threshold_label").html("D' &ge;");
-    });
-
-    // LDtrait change R2/D' threshold label
-    $("#ldtrait_ld_r2").click(function(e){
-        // console.log("R2");
-        $("#ldtrait_r2_d_threshold_label").html("R<sup>2</sup>:");
-    });
-    $("#ldtrait_ld_d").click(function(e){
-        // console.log("D");
-        $("#ldtrait_r2_d_threshold_label").html("D':");
-    });
+$(document).ready(function () {
+	// Close URL change alert banner after 5 seconds
+	$('#url-alert')
+		.delay(5000)
+		.slideUp(600, function () {
+			$(this).alert('close');
+		});
+
+	// Load news text from news.html to news-container div
+	$.get('news.html?v=5.6.0', function (data) {
+		let tmpData = data.split('<p>');
+		let i = 0;
+		var newsHTMLList = [];
+
+		for (i = 1; i < tmpData.length; i++) {
+			let toPush = '<p>' + tmpData[i];
+			newsHTMLList.push(toPush);
+		}
+
+		let lastNews = '';
+		let versionNews = newsHTMLList[0].replace('<br>', '');
+		let numFound = 0;
+		for (let i = 0; i < 1; i++) {
+			if (versionNews.indexOf('</li>') != -1) {
+				lastNews += versionNews.substring(0, versionNews.indexOf('</li>') + 5);
+				versionNews = versionNews.substring(versionNews.indexOf('</li>') + 6);
+				numFound += 1;
+			} else {
+				i = 1;
+			}
+		}
+		if (versionNews.indexOf('</li>') != -1) {
+			lastNews += '</ul> <a class="version-link">Show more...</a>';
+		}
+		lastNews =
+			lastNews.substring(0, lastNews.indexOf('<ul>') + 3) +
+			' style="padding-left:10px; margin-bottom:0;"' +
+			lastNews.substring(lastNews.indexOf('<ul>') + 3);
+		// console.log(lastNews);
+
+		newsList.push(
+			lastNews +
+				'<p style="margin-bottom:0px; margin-top:5px;">(See <a class="version-link">Version History</a>)</p>'
+		);
+		newsList.push(
+			'<p><b>LDlinkR</b><br></p><div style="height:4px;"/><p style="margin:0;">Interested in accessing LDlink\'s API using R? <br style="margin-bottom:5px;">Check out the new LDlinkR package now available on <a href="https://cran.r-project.org/web/packages/LDlinkR/index.html" title="LDlinkR CRAN" target="_blank">CRAN</a>.</p>'
+		);
+		newsList.push(
+			'<p><b>GWAS Explorer</b><br></p><div style="height:4px;"/><p>Visualize and interact with genome-wide association study results from PLCO Atlas.</b> <br style="margin-bottom:5px;">Check out <a href="https://exploregwas.cancer.gov/plco-atlas/" title="GWAS Explorer" target="_blank">GWAS Explorer</a>. </p>'
+		);
+		newsList.push(
+			'<p><b>AuthorArranger</b><br></p><div style="height:4px;"/><p>Bogged down organizing authors and affiliations on journal title pages for large studies?</b> <br style="margin-bottom:5px;">Check out <a href="https://authorarranger.nih.gov/" title="Author Arranger" target="_blank">AuthorArranger</a> and conquer title pages in seconds! </p>'
+		);
+
+		$('#news-card-1').html(newsList[0].replace('<br>', ''));
+		$('#news-card-2').html(newsList[1]);
+		$('#news-card-3').html(newsList[2]);
+		// console.log(newsList)
+		testResize();
+		$('.version-link').on('click', function () {
+			$('#version-tab-anchor').click();
+			window.scrollTo(0, 0);
+		});
+		$('#news-container').append(data);
+	});
+
+	$('#progressbar').progressbar();
+	//$('#progressbar').progressbar('setPosition', 85);
+	//$('#ldassoc-progressbar').progressbar('reset');
+	$('#ldassoc-progressbar').on('positionChanged', function (e) {
+		console.log(e.position);
+		console.log(e.percent);
+	});
+
+	$(':file').change(function () {
+		var file = this.files[0];
+		var name = file.name;
+		var size = file.size;
+		var type = file.type;
+		//Your validation
+		console.dir(file);
+	});
+	$.each(dropdowns, function (i, id) {
+		$('#' + id + ' > .dropdown-menu').on('click', 'li a', function () {
+			createCookie(id, $(this).text(), 10);
+			setBootstrapSelector(id, $(this).text());
+		});
+	});
+	$('#assoc-region > .dropdown-menu li a').click(function (e) {
+		$('#assoc-region > .btn:first-child').html(
+			$(this).text() + '&nbsp;<span class="caret"></span>'
+		);
+		$('#assoc-region > .btn:first-child').val($(this).text().toLowerCase());
+		$('#region-gene-container').hide();
+		$('#region-region-container').hide();
+		$('#region-variant-container').hide();
+		console.log(e.target.id);
+		switch ($(this).text()) {
+			case 'Gene':
+				$('#region-gene-name').val('');
+				// $("#region-gene-base-pair-window").val('');
+				$('#region-gene-index').val('');
+				$('#region-region-start-coord').val('');
+				$('#region-region-end-coord').val('');
+				$('#region-region-index').val('');
+				$('#region-variant-index').val('');
+				// $("#region-variant-base-pair-window").val('');
+				$('#region-gene-container').show();
+				break;
+			case 'Region':
+				$('#region-gene-name').val('');
+				// $("#region-gene-base-pair-window").val('');
+				$('#region-gene-index').val('');
+				$('#region-region-start-coord').val('');
+				$('#region-region-end-coord').val('');
+				$('#region-region-index').val('');
+				$('#region-variant-index').val('');
+				// $("#region-variant-base-pair-window").val('');
+				$('#region-region-container').show();
+				break;
+			case 'Variant':
+				$('#region-gene-name').val('');
+				// $("#region-gene-base-pair-window").val('');
+				$('#region-gene-index').val('');
+				$('#region-region-start-coord').val('');
+				$('#region-region-end-coord').val('');
+				$('#region-region-index').val('');
+				$('#region-variant-index').val('');
+				// $("#region-variant-base-pair-window").val('');
+				$('#region-variant-container').show();
+				break;
+		}
+	});
+
+	// init genome build selection
+	switch (genomeBuild) {
+		case 'grch37':
+			$(document).ready(function () {
+				$('#genome-build > .dropdown-menu li a')[0].click();
+			});
+			break;
+		case 'grch38':
+			$(document).ready(function () {
+				$('#genome-build > .dropdown-menu li a')[1].click();
+			});
+			break;
+		case 'grch38_high_coverage':
+			$(document).ready(function () {
+				$('#genome-build > .dropdown-menu li a')[2].click();
+			});
+			break;
+		default:
+			$(document).ready(function () {
+				$('#genome-build > .dropdown-menu li a')[0].click();
+			});
+	}
+
+	$('#genome-build > .dropdown-menu li a').click(function (e) {
+		$('#genome-build > .btn:first-child').html(
+			$(this).text() + '&nbsp;<span class="caret"></span>'
+		);
+		$('#genome-build > .btn:first-child').val($(this).text().toLowerCase());
+		// console.log($(this).attr("value"));
+		genomeBuild = $(this).attr('value');
+		// change ldassoc example inputs
+		if (document.getElementById('example-gwas').checked) {
+			setupLDassocExample();
+		}
+	});
+
+	// Hide Genome Build dropdown on LD Tools dropdown-nav hover
+	dropdownTools = document.querySelector('#dropdown-tools');
+	dropdownTools.addEventListener('mouseover', (event) => {
+		$('#genome-build').click();
+	});
+
+	$('#ldassoc').prop('disabled', true);
+
+	// reset apiaccess form
+	$('.apiaccess-done').click(function (e) {
+		$('#apiaccess-reset').click();
+		$('#apiaccess-new-user').modal('hide');
+		$('#apiaccess-existing-user').modal('hide');
+
+		$('#apiblocked-form').show();
+		$('#apiblocked').show();
+		$('#apiblocked-submit-message').hide();
+		$('#apiblocked-done').val('Cancel');
+
+		$('#apiblocked-reset').click();
+		$('#apiaccess-blocked-user').modal('hide');
+	});
+
+	$('#example-gwas').click(function (e) {
+		setupLDassocExample();
+	});
+
+	updateVersion(ldlink_version);
+	//addValidators();
+	$('#ldlink-tabs').on('click', 'a', function (e) {
+		// console.warn("You clicked a tab");
+
+		//console.info("Check for an attribute called data-url");
+		//If data-url use that.
+		var currentTab = e.target.id.substr(0, e.target.id.search('-'));
+		// console.log('currentTab: ' + currentTab)
+		clearTabs(currentTab);
+		//console.log(currentTab);
+		var last_url_params = $('#' + currentTab + '-tab-anchor').attr(
+			'data-url-params'
+		);
+		//console.log("last_url_params: "+last_url_params);
+		if (typeof last_url_params === 'undefined') {
+			window.history.pushState({}, '', '?tab=' + currentTab);
+		} else {
+			window.history.pushState({}, '', '?' + last_url_params);
+		}
+	});
+
+	setupLDexpressControls();
+	setupLDtraitControls();
+	setupSNPclipControls();
+	setupSNPchipControls();
+	showFFWarning();
+
+	createAssocTable();
+	createPopTable();
+	createProxyTable();
+	createExpressDetailsTable();
+	createExpressQueryWarningsTable();
+	createTraitDetailsTable();
+	createTraitQueryWarningsTable();
+	var new_assoc_data = {
+		aaData: [
+			[
+				'rs75563749',
+				'chr7',
+				'24958977',
+				'(C/T)',
+				'0.2037',
+				-726,
+				'0.234',
+				'0.234',
+				'C-C',
+				'0.0',
+				'10',
+				'7',
+				'HaploReg link',
+				'NA',
+			],
+			[
+				'rs95696732',
+				'chr4',
+				'24958977',
+				'(C/T)',
+				'0.2037',
+				-726,
+				'1.0',
+				'1.0',
+				'T-T',
+				'0.0',
+				'',
+				'7',
+				'HaploReg link',
+				'NA',
+			],
+		],
+	};
+
+	var new_proxy_data = {
+		aaData: [
+			[
+				'rs125',
+				'chr7',
+				'24958977',
+				'(C/T)',
+				'0.2037',
+				-726,
+				'1.0',
+				'1.0',
+				'C-C,T-T',
+				'8',
+				'7',
+				'HaploReg link',
+				'NA',
+			],
+			[
+				'rs128',
+				'chr7',
+				'24958977',
+				'(C/T)',
+				'0.2037',
+				-726,
+				'1.0',
+				'1.0',
+				'C-C,T-T',
+				'9',
+				'7',
+				'HaploReg link',
+				'NA',
+			],
+			[
+				'.',
+				'chr4',
+				'24958977',
+				'(C/T)',
+				'0.2037',
+				-726,
+				'1.0',
+				'1.0',
+				'C-C,T-T',
+				'9',
+				'7',
+				'HaploReg link',
+				'NA',
+			],
+		],
+	};
+
+	// var new_trait_data = {
+	//     "aaData": [
+	//         ["cognitive function measurement","rs77052120","chr1:110765398","Variant found in GWAS catalog within window."],
+	//     ]
+	// };
+
+	RefreshTable('#new-ldassoc', new_assoc_data);
+	RefreshTable('#new-ldproxy', new_proxy_data);
+
+	$('[data-toggle="popover"]').popover();
+
+	loadHelp();
+
+	// Apply Bindings
+	ko.applyBindings(
+		ldpairModel,
+		document.getElementById('ldpair-results-container')
+	);
+	ko.applyBindings(
+		ldhapModel,
+		document.getElementById('ldhap-results-container')
+	);
+	ko.applyBindings(
+		snpclipModel,
+		document.getElementById('snpclip-results-container')
+	);
+	ko.applyBindings(
+		snpchipModel,
+		document.getElementById('snpchip-results-container')
+	);
+
+	$.each(modules, function (key, id) {
+		buildPopulationDropdown(id + '-population-codes');
+		$('#' + id + '-results-container').hide();
+		$('#' + id + '-message').hide();
+		$('#' + id + '-message-warning').hide();
+		$('#' + id + '-loading').hide();
+	});
+
+	$('#apiblocked-loading').hide();
+	$('#apiblocked-message').hide();
+	$('#apiblocked-message-warning').hide();
+
+	$('.ldlinkForm').on('submit', function (e) {
+		calculate(e);
+	});
+
+	$('.help-anchor-link').on('click', function (e) {
+		var tab = e.target.hash;
+		$('#help-tab-anchor').click();
+		setTimeout(function () {
+			window.location = tab;
+		}, 500);
+		window.scrollTo(0, 0);
+	});
+
+	$('.anchor-link').on('click', function (e) {
+		var tab = $(this).attr('dest');
+		$('#' + tab + '-tab-anchor').click();
+		window.scrollTo(0, 0);
+	});
+
+	setupTabs();
+
+	autoCalculate();
+	createFileSelectEvent();
+	createEnterEvent();
+	initAPIExamples();
+	// Google Maps API
+	initMap();
+	// export LDpop map dropdown buttons
+	$('#ldpop-LD-downloadPNG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop LD map export png");
+		exportMap(1, 'LD', 'png');
+	});
+	$('#ldpop-LD-downloadJPEG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop LD export jpeg");
+		exportMap(1, 'LD', 'jpeg');
+	});
+	// export variant 1 allele freq map
+	$('#ldpop-AFvar1-downloadPNG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop variant 1 allele freq map export png");
+		exportMap(2, 'AF', 'png');
+	});
+	$('#ldpop-AFvar1-downloadJPEG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop variant 1 allele freq map export jpeg");
+		exportMap(2, 'AF', 'jpeg');
+	});
+	// export variant 2 allele freq map
+	$('#ldpop-AFvar2-downloadPNG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop variant 2 allele freq map export png");
+		exportMap(3, 'AF', 'png');
+	});
+	$('#ldpop-AFvar2-downloadJPEG').click(function (e) {
+		e.preventDefault();
+		// console.log("ldpop variant 2 allele freq map export jpeg");
+		exportMap(3, 'AF', 'jpeg');
+	});
+
+	// LDexpress change R2/D' threshold label
+	$('#ldexpress_ld_r2').click(function (e) {
+		// console.log("R2");
+		$('#ldexpress_r2_d_threshold_label').html('R<sup>2</sup> &ge;');
+	});
+	$('#ldexpress_ld_d').click(function (e) {
+		// console.log("D");
+		$('#ldexpress_r2_d_threshold_label').html("D' &ge;");
+	});
+
+	// LDtrait change R2/D' threshold label
+	$('#ldtrait_ld_r2').click(function (e) {
+		// console.log("R2");
+		$('#ldtrait_r2_d_threshold_label').html('R<sup>2</sup>:');
+	});
+	$('#ldtrait_ld_d').click(function (e) {
+		// console.log("D");
+		$('#ldtrait_r2_d_threshold_label').html("D':");
+	});
 });
 
 // Set file support trigger
-$(document).on('change','.btn-snp :file', createFileSelectTrigger);
+$(document).on('change', '.btn-snp :file', createFileSelectTrigger);
 // ldAssoc File Change
-$(document).on('change','.btn-csv-file :file', createFileSelectTrigger);
-
+$(document).on('change', '.btn-csv-file :file', createFileSelectTrigger);
 
 function setupLDassocExample() {
-    //   console.log("Use example GWAS data.");
-    var useEx = document.getElementById('example-gwas');
-    // var exampleHeaders = ['A', 'B', 'C'];
-    if (useEx.checked){
-      var url = restServerUrl + "/ldassoc_example";
-      var ajaxRequest = $.ajax({
-          type : 'GET',
-          url : url,
-          contentType : 'application/json', // JSON
-          data: {
-              genome_build: genomeBuild
-          }
-      }).success(function(response) {
-        var data = JSON.parse(response);
-        $('#ldassoc-file-label').val(data.filename);
-        populateAssocDropDown(data.headers);
-        $("#header-values").show();
-        $("#assoc-chromosome > button").val("chr");
-        $("#assoc-chromosome > button").text("Chromosome: chr column");
-        $("#assoc-position > button").val("pos");
-        $("#assoc-position > button").text("Position: pos column");
-        $("#assoc-p-value > button").val("p");
-        $("#assoc-p-value > button").text("P-Value: p column");
-        $('#ldassoc-file').prop('disabled', true);
-        $('#ldassoc').removeAttr('disabled');
-      });
-
-      $('#region-gene-name').val('');
-      $('#region-gene-index').val('');
-      $('#region-variant-index').val('');
-
-      $("#assoc-region > .btn:first-child").val("Region".toLowerCase());
-      $("#assoc-region > .btn:first-child").html("Region" + '&nbsp;<span class="caret"></span>');
-
-      $("#region-gene-container").hide();
-      $("#region-region-container").hide();
-      $("#region-variant-container").hide();
-      $("#region-region-container").show();
-      switch(genomeBuild) {
-          case "grch37":
-              $("#region-region-start-coord").val("chr8:128289591");
-              $("#region-region-end-coord").val("chr8:128784397");
-              break;
-          case "grch38":
-              $("#region-region-start-coord").val("chr8:127277115");
-              $("#region-region-end-coord").val("chr8:127777115");
-              break;
-          case "grch38_high_coverage":
-              $("#region-region-start-coord").val("chr8:127277115");
-              $("#region-region-end-coord").val("chr8:127777115");
-              break;
-      }
-      $("#region-region-index").val("rs7837688");
-      // console.log($("#region-region-start-coord").val());
-      // console.log($("#region-region-end-coord").val());
-      // console.log($("#region-region-index").val());
-
-      $("#ldassoc-population-codes").val('');
-      refreshPopulation([],"ldassoc");
-      $("#ldassoc-population-codes").val(["CEU"]);
-      refreshPopulation(["CEU"],"ldassoc");
-      // console.log($("#ldassoc-population-codes").val());
-    }else{
-      $('#ldassoc-file').prop('disabled', false);
-      $('#ldassoc').prop('disabled', true);
-      $("#assoc-chromosome > button").val('');
-      $("#assoc-chromosome > button").html('Select Chromosome&nbsp;<span class="caret"></span>');
-      $("#assoc-position > button").val('');
-      $("#assoc-position > button").html('Select Position&nbsp;<span class="caret"></span>');
-      $("#assoc-p-value > button").val('');
-      $("#assoc-p-value > button").html('Select P-Value&nbsp;<span class="caret"></span>');
-
-      $('#ldassoc-file-label').val('');
-      populateAssocDropDown([]);
-      $("#header-values").hide();
-      $('#ldassoc-file').val('');
-      // console.log("Don't use example GWAS data.");
-      $("#region-gene-container").hide();
-      $("#region-region-container").hide();
-      $("#region-variant-container").hide();
-      $("#assoc-region > .btn:first-child").val('');
-      $("#assoc-region > .btn:first-child").html('Select Region<span class="caret"></span>');
-      $("#region-region-start-coord").val('');
-      $("#region-region-end-coord").val('');
-      $("#region-region-index").val('');
-      $("#ldassoc-population-codes").val('');
-      refreshPopulation([],"ldassoc");
-    }
+	//   console.log("Use example GWAS data.");
+	var useEx = document.getElementById('example-gwas');
+	// var exampleHeaders = ['A', 'B', 'C'];
+	if (useEx.checked) {
+		var url = restServerUrl + '/ldassoc_example';
+		var ajaxRequest = $.ajax({
+			type: 'GET',
+			url: url,
+			contentType: 'application/json', // JSON
+			data: {
+				genome_build: genomeBuild,
+			},
+		}).success(function (response) {
+			var data = JSON.parse(response);
+			$('#ldassoc-file-label').val(data.filename);
+			populateAssocDropDown(data.headers);
+			$('#header-values').show();
+			$('#assoc-chromosome > button').val('chr');
+			$('#assoc-chromosome > button').text('Chromosome: chr column');
+			$('#assoc-position > button').val('pos');
+			$('#assoc-position > button').text('Position: pos column');
+			$('#assoc-p-value > button').val('p');
+			$('#assoc-p-value > button').text('P-Value: p column');
+			$('#ldassoc-file').prop('disabled', true);
+			$('#ldassoc').removeAttr('disabled');
+		});
+
+		$('#region-gene-name').val('');
+		$('#region-gene-index').val('');
+		$('#region-variant-index').val('');
+
+		$('#assoc-region > .btn:first-child').val('Region'.toLowerCase());
+		$('#assoc-region > .btn:first-child').html(
+			'Region' + '&nbsp;<span class="caret"></span>'
+		);
+
+		$('#region-gene-container').hide();
+		$('#region-region-container').hide();
+		$('#region-variant-container').hide();
+		$('#region-region-container').show();
+		switch (genomeBuild) {
+			case 'grch37':
+				$('#region-region-start-coord').val('chr8:128289591');
+				$('#region-region-end-coord').val('chr8:128784397');
+				break;
+			case 'grch38':
+				$('#region-region-start-coord').val('chr8:127277115');
+				$('#region-region-end-coord').val('chr8:127777115');
+				break;
+			case 'grch38_high_coverage':
+				$('#region-region-start-coord').val('chr8:127277115');
+				$('#region-region-end-coord').val('chr8:127777115');
+				break;
+		}
+		$('#region-region-index').val('rs7837688');
+		// console.log($("#region-region-start-coord").val());
+		// console.log($("#region-region-end-coord").val());
+		// console.log($("#region-region-index").val());
+
+		$('#ldassoc-population-codes').val('');
+		refreshPopulation([], 'ldassoc');
+		$('#ldassoc-population-codes').val(['CEU']);
+		refreshPopulation(['CEU'], 'ldassoc');
+		// console.log($("#ldassoc-population-codes").val());
+	} else {
+		$('#ldassoc-file').prop('disabled', false);
+		$('#ldassoc').prop('disabled', true);
+		$('#assoc-chromosome > button').val('');
+		$('#assoc-chromosome > button').html(
+			'Select Chromosome&nbsp;<span class="caret"></span>'
+		);
+		$('#assoc-position > button').val('');
+		$('#assoc-position > button').html(
+			'Select Position&nbsp;<span class="caret"></span>'
+		);
+		$('#assoc-p-value > button').val('');
+		$('#assoc-p-value > button').html(
+			'Select P-Value&nbsp;<span class="caret"></span>'
+		);
+
+		$('#ldassoc-file-label').val('');
+		populateAssocDropDown([]);
+		$('#header-values').hide();
+		$('#ldassoc-file').val('');
+		// console.log("Don't use example GWAS data.");
+		$('#region-gene-container').hide();
+		$('#region-region-container').hide();
+		$('#region-variant-container').hide();
+		$('#assoc-region > .btn:first-child').val('');
+		$('#assoc-region > .btn:first-child').html(
+			'Select Region<span class="caret"></span>'
+		);
+		$('#region-region-start-coord').val('');
+		$('#region-region-end-coord').val('');
+		$('#region-region-index').val('');
+		$('#ldassoc-population-codes').val('');
+		refreshPopulation([], 'ldassoc');
+	}
 }
 
 // wait for svg genreation subprocess complete before enabling plot export menu button
 function checkFile(id, fileURL, retries) {
-    // add countdown retries here to prevent hang up of infinite loop
-    fileURL = fileURL.replace("LDlinkRestWeb/tmp/", '');
-    if (retries > 0) {
-        var countdown = retries - 1
-        $.ajax({
-            // type : 'GET',
-            url : '/LDlinkRestWeb/status' + fileURL + '?_=' + new Date().getTime(),
-            contentType : 'application/json', // JSON
-            cache: false
-        }).done(function(response) {
-            if (response) {
-                $('#' + id + "-menu1").html('Export Plot <span class="caret"></span>');
-                $('#' + id + "-menu1").prop('disabled', false);
-            } else {
-                setTimeout(function() { 
-                    checkFile(id, fileURL, countdown); 
-                }, 5000);
-            } 
-        });
-    } else {
-        $('#' + id + "-menu1").html('Export Failed');
-        $('#' + id + "-menu1").prop('disabled', true);
-    }
+	// add countdown retries here to prevent hang up of infinite loop
+	fileURL = fileURL.replace('LDlinkRestWeb/tmp/', '');
+	if (retries > 0) {
+		var countdown = retries - 1;
+		$.ajax({
+			// type : 'GET',
+			url: '/LDlinkRestWeb/status' + fileURL + '?_=' + new Date().getTime(),
+			contentType: 'application/json', // JSON
+			cache: false,
+		}).done(function (response) {
+			if (response) {
+				$('#' + id + '-menu1').html('Export Plot <span class="caret"></span>');
+				$('#' + id + '-menu1').prop('disabled', false);
+			} else {
+				setTimeout(function () {
+					checkFile(id, fileURL, countdown);
+				}, 5000);
+			}
+		});
+	} else {
+		$('#' + id + '-menu1').html('Export Failed');
+		$('#' + id + '-menu1').prop('disabled', true);
+	}
 }
 function initAPIExamples() {
-    $(".apiaccess-examples").each( function(index) { 
-        $(".apiaccess-examples")[index].innerText = $(".apiaccess-examples")[index].innerText.replace('https://ldlink.nih.gov', window.location.origin);
-    });
+	$('.apiaccess-examples').each(function (index) {
+		$('.apiaccess-examples')[index].innerText = $('.apiaccess-examples')[
+			index
+		].innerText.replace('https://ldlink.nih.gov', window.location.origin);
+	});
 }
 function setBootstrapSelector(id, value) {
-    var str = id.substr(6);
-    str = str.toLowerCase().replace(/\b[a-z]/g, function(letter) {
-        return letter.toUpperCase();
-    });
-    var msg = str+": "+value+" column";
-    $("#"+id+" > .btn:first-child").text(msg);
-    $("#"+id+" > .btn:first-child").val(value);
+	var str = id.substr(6);
+	str = str.toLowerCase().replace(/\b[a-z]/g, function (letter) {
+		return letter.toUpperCase();
+	});
+	var msg = str + ': ' + value + ' column';
+	$('#' + id + ' > .btn:first-child').text(msg);
+	$('#' + id + ' > .btn:first-child').val(value);
 }
 function resetBootstrapSelector(id) {
-    var str = id.substr(6);
-    str = str.toLowerCase().replace(/\b[a-z]/g, function(letter) {
-        return letter.toUpperCase();
-    });
-    var msg = "Select "+str+'&nbsp;<span class="caret"></span>';
-    $("#"+id+" > .btn:first-child").html(msg);
-    $("#"+id+" > .btn:first-child").val("");
+	var str = id.substr(6);
+	str = str.toLowerCase().replace(/\b[a-z]/g, function (letter) {
+		return letter.toUpperCase();
+	});
+	var msg = 'Select ' + str + '&nbsp;<span class="caret"></span>';
+	$('#' + id + ' > .btn:first-child').html(msg);
+	$('#' + id + ' > .btn:first-child').val('');
 }
 
 function createFileSelectTrigger() {
-    // console.log("createFileSelectTrigger");
-    var input = $(this), numFiles = input.get(0).files ?
-    input.get(0).files.length : 1, label = input.val().replace(/\\/g, '/').replace(/.*\//, '');
-    input.trigger('fileselect', [numFiles, label]);
+	// console.log("createFileSelectTrigger");
+	var input = $(this),
+		numFiles = input.get(0).files ? input.get(0).files.length : 1,
+		label = input.val().replace(/\\/g, '/').replace(/.*\//, '');
+	input.trigger('fileselect', [numFiles, label]);
 }
 
 function createEnterEvent() {
-    $("body").keypress(function(e) {
-        // Look for a return value
-        var code = e.keyCode || e.which;
-        if (code == 13) { // User pressed return key
-            //console.dir($(e.target));
-            if ($(e.target).attr('role') == 'document') {
-                //alert("You pressed return.  Let's find what is the active tab...");
-                var active_tab = $("div.tab-pane.active").attr('id');
-                //console.log(active_tab);
-                //console.log("Trigger a submit");
-                var tab = active_tab.split("-");
-                var formId = tab[0] + "Form";
-                var pop_codes = tab[0]+"-population-codes";
-                //console.log($("#"+pop_codes).parent().find("div.btn-group").hasClass("open"));
-                $("#"+pop_codes).parent().find("div.btn-group").removeClass("open");
-                $("#"+formId).trigger("submit");
-            }
-        }
-    });
+	$('body').keypress(function (e) {
+		// Look for a return value
+		var code = e.keyCode || e.which;
+		if (code == 13) {
+			// User pressed return key
+			//console.dir($(e.target));
+			if ($(e.target).attr('role') == 'document') {
+				//alert("You pressed return.  Let's find what is the active tab...");
+				var active_tab = $('div.tab-pane.active').attr('id');
+				//console.log(active_tab);
+				//console.log("Trigger a submit");
+				var tab = active_tab.split('-');
+				var formId = tab[0] + 'Form';
+				var pop_codes = tab[0] + '-population-codes';
+				//console.log($("#"+pop_codes).parent().find("div.btn-group").hasClass("open"));
+				$('#' + pop_codes)
+					.parent()
+					.find('div.btn-group')
+					.removeClass('open');
+				$('#' + formId).trigger('submit');
+			}
+		}
+	});
 }
 
 function uploadFile2() {
-
-
-    restService.route = 'LDlinkRestWeb';
-    restServerUrl = restService.protocol + "//" + restService.hostname + restService.pathname + restService.route;
-
-    var filename = $("#ldassocFile").val();
-    // console.log(filename);
-
-    var fileInput = document.getElementById('ldassoc-file');
-    var file = fileInput.files[0];
-    var formData = new FormData();
-    //console.log("formData before");
-    //console.dir(formData);
-    formData.append('ldassocFile', file);
-    //console.log("formData after");
-    //console.dir(formData);
-    // Display the keys
-    //  for (var key of formData.keys()) {
-    //     console.log(key);
-    //  }
-    $.ajax({
-        url: restServerUrl+'/upload',  //Server script to process data
-        type: 'POST',
-        xhr: function() {  // Custom XMLHttpRequest
-            var myXhr = $.ajaxSettings.xhr();
-            if(myXhr.upload){ // Check if upload property exists
-                myXhr.upload.addEventListener('progress',progressHandlingFunction, false); // For handling the progress of the upload
-            }
-            return myXhr;
-        },
-        //Ajax events
-        beforeSend: beforeSendHandler,
-        success: completeHandler,
-        error: errorHandler,
-        // Form data
-        data: formData,
-        //Options to tell jQuery not to process data or worry about content-type.
-        cache: false,
-        contentType: false,
-        processData: false
-    });
-}
-
-function progressHandlingFunction(e){
-
-    if(e.lengthComputable){
-        //$('progress').attr({value:e.loaded,max:e.total});
-        var percent = Math.floor(e.loaded/e.total*100);
-        $( "#progressbar" ).progressbar({value: percent});
-        $( "#progressbar" ).css('width', percent+"%");
-        $( "#progressbar" ).html(percent+'% Completed');
-
-    }
+	restService.route = 'LDlinkRestWeb';
+	restServerUrl =
+		restService.protocol +
+		'//' +
+		restService.hostname +
+		restService.pathname +
+		restService.route;
+
+	var filename = $('#ldassocFile').val();
+	// console.log(filename);
+
+	var fileInput = document.getElementById('ldassoc-file');
+	var file = fileInput.files[0];
+	var formData = new FormData();
+	//console.log("formData before");
+	//console.dir(formData);
+	formData.append('ldassocFile', file);
+	//console.log("formData after");
+	//console.dir(formData);
+	// Display the keys
+	//  for (var key of formData.keys()) {
+	//     console.log(key);
+	//  }
+	$.ajax({
+		url: restServerUrl + '/upload', //Server script to process data
+		type: 'POST',
+		xhr: function () {
+			// Custom XMLHttpRequest
+			var myXhr = $.ajaxSettings.xhr();
+			if (myXhr.upload) {
+				// Check if upload property exists
+				myXhr.upload.addEventListener(
+					'progress',
+					progressHandlingFunction,
+					false
+				); // For handling the progress of the upload
+			}
+			return myXhr;
+		},
+		//Ajax events
+		beforeSend: beforeSendHandler,
+		success: completeHandler,
+		error: errorHandler,
+		// Form data
+		data: formData,
+		//Options to tell jQuery not to process data or worry about content-type.
+		cache: false,
+		contentType: false,
+		processData: false,
+	});
+}
+
+function progressHandlingFunction(e) {
+	if (e.lengthComputable) {
+		//$('progress').attr({value:e.loaded,max:e.total});
+		var percent = Math.floor((e.loaded / e.total) * 100);
+		$('#progressbar').progressbar({ value: percent });
+		$('#progressbar').css('width', percent + '%');
+		$('#progressbar').html(percent + '% Completed');
+	}
 }
 function beforeSendHandler() {
-    console.warn('beforeSendHandler');
-    var percent = 0;
-    $( "#progressbar" ).css('width', percent+"%");
-    $( "#progressbar" ).html(percent+'% Completed');
-    $('#ldassoc-file-container').hide();
-    $('#progressbar').parent().show();
+	console.warn('beforeSendHandler');
+	var percent = 0;
+	$('#progressbar').css('width', percent + '%');
+	$('#progressbar').html(percent + '% Completed');
+	$('#ldassoc-file-container').hide();
+	$('#progressbar').parent().show();
 }
 function completeHandler() {
-    console.warn('completeHandler');
-    $('#progressbar').parent().hide();
-    $('#ldassoc-file-container').fadeIn(1000);
-    // enable calculate button only when file is successfully uploaded
-    $('#ldassoc').removeAttr('disabled');
+	console.warn('completeHandler');
+	$('#progressbar').parent().hide();
+	$('#ldassoc-file-container').fadeIn(1000);
+	// enable calculate button only when file is successfully uploaded
+	$('#ldassoc').removeAttr('disabled');
 }
 function errorHandler(e) {
-    showCommError(e);
-    console.warn('errorHandler');
-    $('#progressbar').parent().hide();
-    $('#ldassoc-file-container').fadeIn(1000);
-    console.error("Comm Error");
-    console.dir(e);
+	showCommError(e);
+	console.warn('errorHandler');
+	$('#progressbar').parent().hide();
+	$('#ldassoc-file-container').fadeIn(1000);
+	console.error('Comm Error');
+	console.dir(e);
 }
 
 function showCommError(e) {
-    $('#myModal').find('.modal-title').html(e.status + " - " + e.statusText);
-    $('#myModal').find('.modal-body').html(e.responseText);
-    // $('#myModal').find('.modal-body').append("\n File uploaded may have exceeded the size limit.");
-    $("#myModal").modal();
+	$('#myModal')
+		.find('.modal-title')
+		.html(e.status + ' - ' + e.statusText);
+	$('#myModal').find('.modal-body').html(e.responseText);
+	// $('#myModal').find('.modal-body').append("\n File uploaded may have exceeded the size limit.");
+	$('#myModal').modal();
 }
 
 function createFileSelectEvent() {
-    // Add file select file listener
-    $('.btn-snp :file').on('fileselect', function(event, numFiles, label) {
-        // console.log(label);
-        $(this).parents('.input-group').find(':text').val(label);
-        populateTextArea(event, numFiles, label);
-
-    });
-    //Customize for ldAssoc
-    $('.btn-csv-file :file').on('fileselect', function(event, numFiles, label) {
-        // console.log(label);
-        $(this).parents('.input-group').find(':text').val(label);
-        // console.log("Event");
-        populateHeaderValues(event, numFiles, label);
-        uploadFile2();
-        $("#header-values").show();
-        //Changing loadCSVFile because the file size is 722Meg
-        //loadCSVFile(event);
-    });
-}
-
-function fileUpload(fieldName, buttonName){
-
-    restService.route = 'LDlinkRestWeb/load';
-    //restServerUrl = restService.protocol + "//" + restService.hostname + restService.pathname + restService.route;
-    uploadFile(fieldName, buttonName);
+	// Add file select file listener
+	$('.btn-snp :file').on('fileselect', function (event, numFiles, label) {
+		// console.log(label);
+		$(this).parents('.input-group').find(':text').val(label);
+		populateTextArea(event, numFiles, label);
+	});
+	//Customize for ldAssoc
+	$('.btn-csv-file :file').on('fileselect', function (event, numFiles, label) {
+		// console.log(label);
+		$(this).parents('.input-group').find(':text').val(label);
+		// console.log("Event");
+		populateHeaderValues(event, numFiles, label);
+		uploadFile2();
+		$('#header-values').show();
+		//Changing loadCSVFile because the file size is 722Meg
+		//loadCSVFile(event);
+	});
+}
+
+function fileUpload(fieldName, buttonName) {
+	restService.route = 'LDlinkRestWeb/load';
+	//restServerUrl = restService.protocol + "//" + restService.hostname + restService.pathname + restService.route;
+	uploadFile(fieldName, buttonName);
 }
 
 function readSingleFile(evt) {
-    //Retrieve the first (and only!) File from the FileList object
-    var f = evt.target.files[0];
-    if (f) {
-      var r = new FileReader();
-      r.onload = function(e) {
-        // console.log( "Got the file.n"
-        //       +"name: " + f.name + "n"
-        //       +"type: " + f.type + "n"
-        //       +"size: " + f.size + " bytesn"
-        //       + "starts with: "
-        // );
-
-        var contents = e.target.result;
-        var defaults = {
-            separator:' ',
-            delimiter:' ',
-            headers:true
-        };
-        var data = $.csv.toObjects(contents, defaults);
-        console.dir(data);
-      }
-      r.readAsText(f);
-    } else {
-      alert("Failed to load file");
-    }
-  }/*
+	//Retrieve the first (and only!) File from the FileList object
+	var f = evt.target.files[0];
+	if (f) {
+		var r = new FileReader();
+		r.onload = function (e) {
+			// console.log( "Got the file.n"
+			//       +"name: " + f.name + "n"
+			//       +"type: " + f.type + "n"
+			//       +"size: " + f.size + " bytesn"
+			//       + "starts with: "
+			// );
+
+			var contents = e.target.result;
+			var defaults = {
+				separator: ' ',
+				delimiter: ' ',
+				headers: true,
+			};
+			var data = $.csv.toObjects(contents, defaults);
+			console.dir(data);
+		};
+		r.readAsText(f);
+	} else {
+		alert('Failed to load file');
+	}
+} /*
 Action item:
 
 */
 function loadCSVFile(event) {
-    readSingleFile(event);
-    console.warn("Load CSV parse.  Let's take a look at what we got");
-    alert("Hello");
-    var id = event.target.id;
-    if (window.FileReader) {
-
-        var input = event.target;
-        var reader = new FileReader();
-        reader.onload = function() {
-            var text = reader.result;
-            alert(text);
-            var data = $.csv.toObjects(text);
-            alert(text);
-            console.dir(data);
-        };
-    } else {
-        console.warn('FileReader not supported');
-        return;
-    }
+	readSingleFile(event);
+	console.warn("Load CSV parse.  Let's take a look at what we got");
+	alert('Hello');
+	var id = event.target.id;
+	if (window.FileReader) {
+		var input = event.target;
+		var reader = new FileReader();
+		reader.onload = function () {
+			var text = reader.result;
+			alert(text);
+			var data = $.csv.toObjects(text);
+			alert(text);
+			console.dir(data);
+		};
+	} else {
+		console.warn('FileReader not supported');
+		return;
+	}
 }
 
 function createAssocTable() {
-
-    var ldassocTable = $('#new-ldassoc').DataTable( {
-        "bPaginate": true,
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        "order": [[ 9, "asc" ], [ 5, "asc"]], //Order desc on DPrime
-        "columnDefs": [
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_rs_results_link(data, type, row);
-                },
-                "targets": 0
-            },
-            {
-                "render": function ( data, type, row ) {
-                    //Remove 'chr' from the chromosome
-                    return data.substring(3);
-                },
-                "targets": 1
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_position_link(data, type, row);
-                },
-                "targets": 2
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldassoc_FORGEdb_link(data, type, row);
-                },
-                "targets": 10
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_regulome_link(data, type, row);
-                },
-                "targets": 11
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_haploreg_link(data, type, row);
-                },
-                "targets": 12
-            },
-            { className: "dt-body-center", "targets": [ 1, 10, 11,12 ] }
-        ]
-    });
-
+	var ldassocTable = $('#new-ldassoc').DataTable({
+		bPaginate: true,
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		order: [
+			[9, 'asc'],
+			[5, 'asc'],
+		], //Order desc on DPrime
+		columnDefs: [
+			{
+				render: function (data, type, row) {
+					return ldproxy_rs_results_link(data, type, row);
+				},
+				targets: 0,
+			},
+			{
+				render: function (data, type, row) {
+					//Remove 'chr' from the chromosome
+					return data.substring(3);
+				},
+				targets: 1,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_position_link(data, type, row);
+				},
+				targets: 2,
+			},
+			{
+				render: function (data, type, row) {
+					return ldassoc_FORGEdb_link(data, type, row);
+				},
+				targets: 10,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_regulome_link(data, type, row);
+				},
+				targets: 11,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_haploreg_link(data, type, row);
+				},
+				targets: 12,
+			},
+			{ className: 'dt-body-center', targets: [1, 10, 11, 12] },
+		],
+	});
 }
 
 function createPopTable() {
-
-    var ldpopTable = $('#new-ldpop').DataTable( {
-        "aaSorting": [],  /* Disable initial sort */
-        "bPaginate": false,
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": false,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        "columnDefs": [
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to LDpair in final row
-                    return ldpop_ldpair_results_link(data, type, row, genomeBuild);
-                },
-                "targets": 6
-            },
-            { 
-                className: "dt-head-center", 
-                className: "dt-body-center",
-                "targets": [ 0, 1, 2, 3, 4, 5, 6 ] 
-            }
-        ]
-    });
-
+	var ldpopTable = $('#new-ldpop').DataTable({
+		aaSorting: [] /* Disable initial sort */,
+		bPaginate: false,
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: false,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		columnDefs: [
+			{
+				render: function (data, type, row) {
+					// Provide link to LDpair in final row
+					return ldpop_ldpair_results_link(data, type, row, genomeBuild);
+				},
+				targets: 6,
+			},
+			{
+				className: 'dt-head-center',
+				className: 'dt-body-center',
+				targets: [0, 1, 2, 3, 4, 5, 6],
+			},
+		],
+	});
 }
 
 function createProxyTable() {
-
-    var ldproxyTable = $('#new-ldproxy').DataTable( {
-        "bPaginate": true,
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        "order": [[ 7, "desc" ], [ 5, "desc"]], //Order desc on DPrime
-        "columnDefs": [
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_rs_results_link(data, type, row);
-                },
-                "targets": 0
-            },
-            {
-                "render": function ( data, type, row ) {
-                    //Remove 'chr' from the chromosome
-                    return data.substring(3);
-                },
-                "targets": 1
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_position_link(data, type, row);
-                },
-                "targets": 2
-            },
-             {
-                "render": function ( data, type, row ) {
-                    return ldproxy_FORGEdb_link(data, type, row);
-                },
-                "targets": 9
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_regulome_link(data, type, row);
-                },
-                "targets": 10
-            },
-            {
-                "render": function ( data, type, row ) {
-                    return ldproxy_haploreg_link(data, type, row);
-                },
-                "targets": 11
-            },
-            { className: "dt-body-center", "targets": [ 1, 9, 10,11 ] }
-        ]
-    });
-
+	var ldproxyTable = $('#new-ldproxy').DataTable({
+		bPaginate: true,
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		order: [
+			[7, 'desc'],
+			[5, 'desc'],
+		], //Order desc on DPrime
+		columnDefs: [
+			{
+				render: function (data, type, row) {
+					return ldproxy_rs_results_link(data, type, row);
+				},
+				targets: 0,
+			},
+			{
+				render: function (data, type, row) {
+					//Remove 'chr' from the chromosome
+					return data.substring(3);
+				},
+				targets: 1,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_position_link(data, type, row);
+				},
+				targets: 2,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_FORGEdb_link(data, type, row);
+				},
+				targets: 9,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_regulome_link(data, type, row);
+				},
+				targets: 10,
+			},
+			{
+				render: function (data, type, row) {
+					return ldproxy_haploreg_link(data, type, row);
+				},
+				targets: 11,
+			},
+			{ className: 'dt-body-center', targets: [1, 9, 10, 11] },
+		],
+	});
 }
 
 function createExpressDetailsTable() {
-
-    var ldexpressDetailsTable = $('#new-ldexpress').DataTable( {
-        "aaSorting": [],  /* Disable initial sort */
-        "bPaginate": true,
-        // "sScrollY": "600px",
-        // xScrollX: "100%",
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        // "order": [[ 4, "desc" ]], //Order desc on R2
-        "columnDefs": [
-            {
-                // "visible": false,
-                "targets": 0
-            },
-            {
-                "visible": true,
-                "render": function ( data, type, row ) {
-                    // Provide link to gwas catalog
-                    return ldexpress_dbsnp_link(data, type, row);
-                },
-                "targets": 1
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Round floats to 4 decimal places 
-                    if (!isNaN(parseFloat(data))) {
-                        if (parseFloat(data) == 1.0) {
-                            return "1.0";
-                        } else if (parseFloat(data) == 0.0) {
-                            return "0.0";
-                        } else if (parseFloat(data) <= 0.0001) {
-                            return "<0.0001";
-                        } else {
-                            return parseFloat(data).toFixed(3);
-                        }
-                    } else {
-                        return data;
-                    }
-                },
-                "targets": [ 3, 4 ]
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to NCBI
-                    return ldexpress_NCBI_link(data, type, row);
-                },
-                "targets": 5
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to Gencode
-                    return ldexpress_Gencode_link(data, type, row);
-                },
-                "targets": 6
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to Gencode
-                    return ldexpress_GTEx_tissue_link(data, type, row);
-                },
-                "targets": 7
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to GTEx
-                    return ldexpress_GTEx_effect_size_link(data, type, row);
-                },
-                "targets": 10
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to GTEx
-                    return ldexpress_GTEx_pvalue_link(data, type, row);
-                },
-                "targets": 11
-            },
-            { 
-                className: "dt-head-left", 
-                className: "dt-body-left",
-                "targets": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 ] 
-            }
-        ]
-    });
+	var ldexpressDetailsTable = $('#new-ldexpress').DataTable({
+		aaSorting: [] /* Disable initial sort */,
+		bPaginate: true,
+		// "sScrollY": "600px",
+		// xScrollX: "100%",
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		// "order": [[ 4, "desc" ]], //Order desc on R2
+		columnDefs: [
+			{
+				// "visible": false,
+				targets: 0,
+			},
+			{
+				visible: true,
+				render: function (data, type, row) {
+					// Provide link to gwas catalog
+					return ldexpress_dbsnp_link(data, type, row);
+				},
+				targets: 1,
+			},
+			{
+				render: function (data, type, row) {
+					// Round floats to 4 decimal places
+					if (!isNaN(parseFloat(data))) {
+						if (parseFloat(data) == 1.0) {
+							return '1.0';
+						} else if (parseFloat(data) == 0.0) {
+							return '0.0';
+						} else if (parseFloat(data) <= 0.0001) {
+							return '<0.0001';
+						} else {
+							return parseFloat(data).toFixed(3);
+						}
+					} else {
+						return data;
+					}
+				},
+				targets: [3, 4],
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to NCBI
+					return ldexpress_NCBI_link(data, type, row);
+				},
+				targets: 5,
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to Gencode
+					return ldexpress_Gencode_link(data, type, row);
+				},
+				targets: 6,
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to Gencode
+					return ldexpress_GTEx_tissue_link(data, type, row);
+				},
+				targets: 7,
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to GTEx
+					return ldexpress_GTEx_effect_size_link(data, type, row);
+				},
+				targets: 10,
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to GTEx
+					return ldexpress_GTEx_pvalue_link(data, type, row);
+				},
+				targets: 11,
+			},
+			{
+				className: 'dt-head-left',
+				className: 'dt-body-left',
+				targets: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
+			},
+		],
+	});
 }
 
 function createExpressQueryWarningsTable() {
-
-    var ldexpressQueryWarningsTable = $('#new-ldexpress-query-warnings').DataTable( {
-        "aaSorting": [],  /* Disable initial sort */
-        "bPaginate": true,
-        // "sScrollY": "600px",
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        "columnDefs": [
-            { 
-                className: "dt-head-left", 
-                className: "dt-body-left",
-                "targets": [ 0, 1, 2 ] 
-            }
-        ]
-    });
-
+	var ldexpressQueryWarningsTable = $(
+		'#new-ldexpress-query-warnings'
+	).DataTable({
+		aaSorting: [] /* Disable initial sort */,
+		bPaginate: true,
+		// "sScrollY": "600px",
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		columnDefs: [
+			{
+				className: 'dt-head-left',
+				className: 'dt-body-left',
+				targets: [0, 1, 2],
+			},
+		],
+	});
 }
 
-
-
 function createTraitDetailsTable() {
-
-    var ldtraitDetailsTable = $('#new-ldtrait').DataTable( {
-        "aaSorting": [],  /* Disable initial sort */
-        "bPaginate": true,
-        // "sScrollY": "600px",
-        // xScrollX: "100%",
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        // "order": [[ 4, "desc" ]], //Order desc on R2
-        "columnDefs": [
-            {
-                "render": function ( data, type, row ) {
-                    return ldtrait_parse_float(data);
-                },
-                "targets": [ 8 ]
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Round floats to 3 decimal places if string can be parsed to float
-                    if (!isNaN(parseFloat(data))) {
-                        return parseFloat(data).toFixed(3);
-                    } else {
-                        return data;
-                    }
-                },
-                "targets": [ 7 ]
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Round floats to 4 decimal places 
-                    if (type === 'display') {
-                        var floatData  = parseFloat(data);
-                        if (data != "NA" && floatData) {
-                            if (floatData === 1.0) {
-                                return "1.0";
-                            } else if (floatData === 0.0) {
-                                return "0.0";
-                            } else {
-                                var val = floatData.toExponential(0).split(/E/i);
-                                return val[0] + "x10" + val[1].sup();
-                            }
-                        } else {
-                            if (floatData === 0.0 && (data.includes("E") || data.includes("e"))) {
-                                var val = data.split(/E/i);
-                                return val[0] + "x10" + val[1].sup();
-                            } else {
-                                return data;
-                            }
-                        }
-                    } else {
-                        return data;
-                    }
-                },
-                "targets": [ 10 ]
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to LDpair 
-                    var snp1 = row[6][0];
-                    var snp2 = row[6][1];
-                    var pops = row[6][2];
-                    return ldtrait_ldpair_results_link(snp1, snp2, pops, data);
-                },
-                "targets": [ 4, 5 ]
-            },
-            {
-                "bVisible": false,
-                "targets": 6
-            },
-            {
-                "render": function ( data, type, row ) {
-                    // Provide link to gwas catalog
-                    return ldtrait_gwas_catalog_link(data, type, row);
-                },
-                "targets": 11
-            },
-            { 
-                className: "dt-head-left", 
-                className: "dt-body-left",
-                "targets": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 ] 
-            }
-        ]
-    });
+	var ldtraitDetailsTable = $('#new-ldtrait').DataTable({
+		aaSorting: [] /* Disable initial sort */,
+		bPaginate: true,
+		// "sScrollY": "600px",
+		// xScrollX: "100%",
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		// "order": [[ 4, "desc" ]], //Order desc on R2
+		columnDefs: [
+			{
+				render: function (data, type, row) {
+					return ldtrait_parse_float(data);
+				},
+				targets: [8],
+			},
+			{
+				render: function (data, type, row) {
+					// Round floats to 3 decimal places if string can be parsed to float
+					if (!isNaN(parseFloat(data))) {
+						return parseFloat(data).toFixed(3);
+					} else {
+						return data;
+					}
+				},
+				targets: [7],
+			},
+			{
+				render: function (data, type, row) {
+					// Round floats to 4 decimal places
+					if (type === 'display') {
+						var floatData = parseFloat(data);
+						if (data != 'NA' && floatData) {
+							if (floatData === 1.0) {
+								return '1.0';
+							} else if (floatData === 0.0) {
+								return '0.0';
+							} else {
+								var val = floatData.toExponential(0).split(/E/i);
+								return val[0] + 'x10' + val[1].sup();
+							}
+						} else {
+							if (
+								floatData === 0.0 &&
+								(data.includes('E') || data.includes('e'))
+							) {
+								var val = data.split(/E/i);
+								return val[0] + 'x10' + val[1].sup();
+							} else {
+								return data;
+							}
+						}
+					} else {
+						return data;
+					}
+				},
+				targets: [10],
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to LDpair
+					var snp1 = row[6][0];
+					var snp2 = row[6][1];
+					var pops = row[6][2];
+					return ldtrait_ldpair_results_link(snp1, snp2, pops, data);
+				},
+				targets: [4, 5],
+			},
+			{
+				bVisible: false,
+				targets: 6,
+			},
+			{
+				render: function (data, type, row) {
+					// Provide link to gwas catalog
+					return ldtrait_gwas_catalog_link(data, type, row);
+				},
+				targets: 11,
+			},
+			{
+				className: 'dt-head-left',
+				className: 'dt-body-left',
+				targets: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
+			},
+		],
+	});
 }
 
 function createTraitQueryWarningsTable() {
-
-    var ldtraitQueryWarningsTable = $('#new-ldtrait-query-warnings').DataTable( {
-        "aaSorting": [],  /* Disable initial sort */
-        "bPaginate": true,
-        // "sScrollY": "600px",
-        "bJQueryUI": false,  // ThemeRoller
-        "bLengthChange": true,
-        "bFilter": true,
-        "bSort": true,
-        "bInfo": true,
-        "bAutoWidth": true,
-        "bProcessing": false,
-        "deferRender": false,
-        "columnDefs": [
-            { 
-                className: "dt-head-left", 
-                className: "dt-body-left",
-                "targets": [ 0, 1, 2 ] 
-            }
-        ]
-    });
-
+	var ldtraitQueryWarningsTable = $('#new-ldtrait-query-warnings').DataTable({
+		aaSorting: [] /* Disable initial sort */,
+		bPaginate: true,
+		// "sScrollY": "600px",
+		bJQueryUI: false, // ThemeRoller
+		bLengthChange: true,
+		bFilter: true,
+		bSort: true,
+		bInfo: true,
+		bAutoWidth: true,
+		bProcessing: false,
+		deferRender: false,
+		columnDefs: [
+			{
+				className: 'dt-head-left',
+				className: 'dt-body-left',
+				targets: [0, 1, 2],
+			},
+		],
+	});
 }
 
 function setupTabs() {
-    //Clear the active tab on a reload
-    $.each(modules, function(key, id) {
-        $("#"+id+"-tab-anchor").parent().removeClass('active');
-    });
-
-    $("#home-tab-anchor").removeClass('active');
-    $("#help-tab-anchor").removeClass('active');
-    $("#apiaccess-tab-anchor").removeClass('active');
-    //Look for a tab variable on the url
-    var url = "{tab:''}";
-    var search = location.search.substring(1);
-    if(search.length >0 ) {
-        url = JSON.parse('{"' + decodeURI(search).replace(/"/g, '\\"').replace(/&/g, '","').replace(/=/g,'":"').replace(/\n/, '\\\\n').replace(/\t/, '') + '"}');
-    }
-
-    var currentTab;
-    if(typeof url.tab !="undefined") {
-        currentTab = url.tab.toLowerCase();
-    } else {
-        currentTab = 'home';
-        window.history.pushState({},'', "?tab=home");
-    }
-    if(currentTab.search('assoc')>=0) currentTab = 'ldassoc'; 
-    if(currentTab.search('express')>=0) currentTab = 'ldexpress';
-    if(currentTab.search('hap')>=0) currentTab = 'ldhap';
-    if(currentTab.search('matrix')>=0) currentTab = 'ldmatrix';
-    if(currentTab.search('pair')>=0) currentTab = 'ldpair';
-    if(currentTab.search('pop')>=0) currentTab = 'ldpop';
-    if(currentTab.search('proxy')>=0) currentTab = 'ldproxy';
-    if(currentTab.search('trait')>=0) currentTab = 'ldtrait';
-    if(currentTab.search('clip')>=0) currentTab = 'snpclip';
-    if(currentTab.search('chip')>=0) currentTab = 'snpchip';
-    if(currentTab.search('access')>=0) currentTab = 'apiaccess';
-
-    $('#'+currentTab+'-tab').addClass("in").addClass('active');
-    $('#'+currentTab+'-tab-anchor').parent().addClass('active');
-    let found = false;
-    $.each(modules, function(key, id) {
-        if(id==currentTab && id!="apiaccess"){
-            found = true;
-        }
-    });
-    if(found == true){
-        $("#dropdown-tools").addClass("active-link")
-    }
-    else{
-        $("#dropdown-tools").removeClass("active-link")
-    }
-    
-    if(typeof url.inputs !="undefined") {
-        //console.dir(url.inputs.replace(/\t/, '').replace(/\n/, '\\\\n'));
-        updateData(currentTab, url.inputs.replace(/\t/, '').replace(/\n/, '\\\\n'));
-    }
-
-    if (headerModules.includes(currentTab)) {
-        $('#module-header').show();
-        document.getElementById("module-help").href = moduleTitleDescription[currentTab][1];
-        document.getElementById("module-title").childNodes[0].nodeValue = moduleTitleDescription[currentTab][0];
-        document.getElementById("module-description").innerHTML = moduleTitleDescription[currentTab][2];
-    }
-    else {
-        $('#module-header').hide();
-    }
-    
+	//Clear the active tab on a reload
+	$.each(modules, function (key, id) {
+		$('#' + id + '-tab-anchor')
+			.parent()
+			.removeClass('active');
+	});
+
+	$('#home-tab-anchor').removeClass('active');
+	$('#help-tab-anchor').removeClass('active');
+	$('#apiaccess-tab-anchor').removeClass('active');
+	//Look for a tab variable on the url
+	var url = "{tab:''}";
+	var search = location.search.substring(1);
+	if (search.length > 0) {
+		url = JSON.parse(
+			'{"' +
+				decodeURI(search)
+					.replace(/"/g, '\\"')
+					.replace(/&/g, '","')
+					.replace(/=/g, '":"')
+					.replace(/\n/, '\\\\n')
+					.replace(/\t/, '') +
+				'"}'
+		);
+	}
+
+	var currentTab;
+	if (typeof url.tab != 'undefined') {
+		currentTab = url.tab.toLowerCase();
+	} else {
+		currentTab = 'home';
+		window.history.pushState({}, '', '?tab=home');
+	}
+	if (currentTab.search('assoc') >= 0) currentTab = 'ldassoc';
+	if (currentTab.search('express') >= 0) currentTab = 'ldexpress';
+	if (currentTab.search('hap') >= 0) currentTab = 'ldhap';
+	if (currentTab.search('matrix') >= 0) currentTab = 'ldmatrix';
+	if (currentTab.search('pair') >= 0) currentTab = 'ldpair';
+	if (currentTab.search('pop') >= 0) currentTab = 'ldpop';
+	if (currentTab.search('proxy') >= 0) currentTab = 'ldproxy';
+	if (currentTab.search('trait') >= 0) currentTab = 'ldtrait';
+	if (currentTab.search('clip') >= 0) currentTab = 'snpclip';
+	if (currentTab.search('chip') >= 0) currentTab = 'snpchip';
+	if (currentTab.search('access') >= 0) currentTab = 'apiaccess';
+
+	$('#' + currentTab + '-tab')
+		.addClass('in')
+		.addClass('active');
+	$('#' + currentTab + '-tab-anchor')
+		.parent()
+		.addClass('active');
+	let found = false;
+	$.each(modules, function (key, id) {
+		if (id == currentTab && id != 'apiaccess') {
+			found = true;
+		}
+	});
+	if (found == true) {
+		$('#dropdown-tools').addClass('active-link');
+	} else {
+		$('#dropdown-tools').removeClass('active-link');
+	}
+
+	if (typeof url.inputs != 'undefined') {
+		//console.dir(url.inputs.replace(/\t/, '').replace(/\n/, '\\\\n'));
+		updateData(currentTab, url.inputs.replace(/\t/, '').replace(/\n/, '\\\\n'));
+	}
+
+	if (headerModules.includes(currentTab)) {
+		$('#module-header').show();
+		document.getElementById('module-help').href =
+			moduleTitleDescription[currentTab][1];
+		document.getElementById('module-title').childNodes[0].nodeValue =
+			moduleTitleDescription[currentTab][0];
+		document.getElementById('module-description').innerHTML =
+			moduleTitleDescription[currentTab][2];
+	} else {
+		$('#module-header').hide();
+	}
 }
 
 function refreshPopulation(pop, id) {
-
-    $.each(pop, function(key, value){
-        $('option[value="'+value+'"]', $('#'+id+'-population-codes')).prop('selected', true);
-    });
-    $('#'+id+'-population-codes').multiselect('refresh');
-
+	$.each(pop, function (key, value) {
+		$('option[value="' + value + '"]', $('#' + id + '-population-codes')).prop(
+			'selected',
+			true
+		);
+	});
+	$('#' + id + '-population-codes').multiselect('refresh');
 }
 
 function autoCalculate() {
-    // if valid parameters exist in the url then calcluate
-    var url = {};
-    var search = location.search.substring(1);
-    if(search.length >0 ) {
-        url = JSON.parse('{"' + decodeURI(search).replace(/"/g, '\\"').replace(/&/g, '","').replace(/=/g,'":"').replace(/\n/, '\\\\n').replace(/\t/, '') + '"}');
-    }
-    if(typeof url.tab !="undefined") {
-    } else {
-        return;
-    }
-    var id = url.tab.toLowerCase();
-    switch (id) {
-        case "ldpair":
-            if(url.var1 && url.var2 && url.pop) {
-                $("#ldpair-snp1").prop('value', url.var1);
-                $("#ldpair-snp2").prop('value', url.var2);
-                refreshPopulation(decodeURIComponent(url.pop).split("+"), id);
-                initCalculate(id);
-                updateData(id);
-            }
-            break;
-        case "ldpop":
-            if(url.var1 && url.var2 && url.pop && url.r2_d) {
-                $("#ldpop-snp1").prop('value', url.var1);
-                $("#ldpop-snp2").prop('value', url.var2);
-                $("#pop_ld_r2").toggleClass('active', url.r2_d == "r2");
-                $("#pop_ld_r2").next().toggleClass('active', url.r2_d == "d");
-                refreshPopulation(decodeURIComponent(url.pop).split("+"), id);
-                initCalculate(id);
-                updateData(id);
-            }
-            break;
-        case "ldproxy":
-            if(url.var && url.pop && url.r2_d) {
-                $("#ldproxy-snp").prop('value', url.var);
-                $("#proxy_color_r2").toggleClass('active', url.r2_d == "r2");
-                $("#proxy_color_r2").next().toggleClass('active', url.r2_d == "d");
-                refreshPopulation(decodeURIComponent(url.pop).split("+"), id);
-                initCalculate(id);
-                updateData(id);
-            }
-            break;
-    }
+	// if valid parameters exist in the url then calcluate
+	var url = {};
+	var search = location.search.substring(1);
+	if (search.length > 0) {
+		url = JSON.parse(
+			'{"' +
+				decodeURI(search)
+					.replace(/"/g, '\\"')
+					.replace(/&/g, '","')
+					.replace(/=/g, '":"')
+					.replace(/\n/, '\\\\n')
+					.replace(/\t/, '') +
+				'"}'
+		);
+	}
+	if (typeof url.tab != 'undefined') {
+	} else {
+		return;
+	}
+	var id = url.tab.toLowerCase();
+	switch (id) {
+		case 'ldpair':
+			if (url.var1 && url.var2 && url.pop) {
+				$('#ldpair-snp1').prop('value', url.var1);
+				$('#ldpair-snp2').prop('value', url.var2);
+				refreshPopulation(decodeURIComponent(url.pop).split('+'), id);
+				initCalculate(id);
+				updateData(id);
+			}
+			break;
+		case 'ldpop':
+			if (url.var1 && url.var2 && url.pop && url.r2_d) {
+				$('#ldpop-snp1').prop('value', url.var1);
+				$('#ldpop-snp2').prop('value', url.var2);
+				$('#pop_ld_r2').toggleClass('active', url.r2_d == 'r2');
+				$('#pop_ld_r2')
+					.next()
+					.toggleClass('active', url.r2_d == 'd');
+				refreshPopulation(decodeURIComponent(url.pop).split('+'), id);
+				initCalculate(id);
+				updateData(id);
+			}
+			break;
+		case 'ldproxy':
+			if (url.var && url.pop && url.r2_d) {
+				$('#ldproxy-snp').prop('value', url.var);
+				$('#proxy_color_r2').toggleClass('active', url.r2_d == 'r2');
+				$('#proxy_color_r2')
+					.next()
+					.toggleClass('active', url.r2_d == 'd');
+				refreshPopulation(decodeURIComponent(url.pop).split('+'), id);
+				initCalculate(id);
+				updateData(id);
+			}
+			break;
+	}
 }
 
 function setupSNPchipControls() {
-    // Setup click listners for the platform selector
-    $('#accordion').on('hidden.bs.collapse', toggleChevron);
-    $('#accordion').on('shown.bs.collapse', toggleChevron);
-
-    $('#selectAllChipTypes').click(function(e) {
-        if($(".illumina:checked").length == $("input.illumina").length &&
-            $(".affymetrix:checked").length == $("input.affymetrix").length) {
-            $(".illumina").prop("checked", false);
-            $(".affymetrix").prop("checked", false);
-            $("#selectAllIllumina").prop("checked", false);
-            $("#selectAllAffymetrix").prop("checked", false);
-        } else {
-            $(".illumina").prop("checked", true);
-            $(".affymetrix").prop("checked", true);
-            $("#selectAllIllumina").prop("checked", true);
-            $("#selectAllAffymetrix").prop("checked", true);
-        }
-        checkSelectAllCheckbox();
-        calculateChipTotals();
-    });
-
-    $('#selectAllIllumina').click(function(e) {
-        var id = e.target.id;
-        //console.log("Look for state");
-        //console.dir(e);
-        //console.log($("#"+id).prop('checked'));
-        if($("#"+id).prop('checked') == true) {
-            $(".illumina").prop("checked", true);
-        } else {
-            $(".illumina").prop("checked", false);
-        }
-        checkSelectAllCheckbox();
-        calculateChipTotals();
-    });
-    $('#selectAllAffymetrix').click(function(e) {
-        var id = e.target.id;
-        if($("#"+id).prop('checked') == true) {
-            $(".affymetrix").prop("checked", true);
-        } else {
-            $(".affymetrix").prop("checked", false);
-        }
-        checkSelectAllCheckbox();
-        calculateChipTotals();
-    });
-    $('#collapseThree').on('click', "input.illumina, input.affymetrix", function(e) {
-        checkSelectAllCheckbox();
-        calculateChipTotals();
-    });
-    initChip();
+	// Setup click listners for the platform selector
+	$('#accordion').on('hidden.bs.collapse', toggleChevron);
+	$('#accordion').on('shown.bs.collapse', toggleChevron);
+
+	$('#selectAllChipTypes').click(function (e) {
+		if (
+			$('.illumina:checked').length == $('input.illumina').length &&
+			$('.affymetrix:checked').length == $('input.affymetrix').length
+		) {
+			$('.illumina').prop('checked', false);
+			$('.affymetrix').prop('checked', false);
+			$('#selectAllIllumina').prop('checked', false);
+			$('#selectAllAffymetrix').prop('checked', false);
+		} else {
+			$('.illumina').prop('checked', true);
+			$('.affymetrix').prop('checked', true);
+			$('#selectAllIllumina').prop('checked', true);
+			$('#selectAllAffymetrix').prop('checked', true);
+		}
+		checkSelectAllCheckbox();
+		calculateChipTotals();
+	});
+
+	$('#selectAllIllumina').click(function (e) {
+		var id = e.target.id;
+		//console.log("Look for state");
+		//console.dir(e);
+		//console.log($("#"+id).prop('checked'));
+		if ($('#' + id).prop('checked') == true) {
+			$('.illumina').prop('checked', true);
+		} else {
+			$('.illumina').prop('checked', false);
+		}
+		checkSelectAllCheckbox();
+		calculateChipTotals();
+	});
+	$('#selectAllAffymetrix').click(function (e) {
+		var id = e.target.id;
+		if ($('#' + id).prop('checked') == true) {
+			$('.affymetrix').prop('checked', true);
+		} else {
+			$('.affymetrix').prop('checked', false);
+		}
+		checkSelectAllCheckbox();
+		calculateChipTotals();
+	});
+	$('#collapseThree').on(
+		'click',
+		'input.illumina, input.affymetrix',
+		function (e) {
+			checkSelectAllCheckbox();
+			calculateChipTotals();
+		}
+	);
+	initChip();
 }
 
 function checkSelectAllCheckbox() {
-    //Determin if the master checkbox should be checked or not.
-    var illumina = $(".illumina:checked").length;
-    var affymetrix = $(".affymetrix:checked").length;
-    var total_illumina = $("input.illumina").length;
-    var total_affymetrix = $("input.affymetrix").length;
-
-    if(illumina == total_illumina) {
-        $('#selectAllIllumina').prop('checked', true);
-    } else {
-        $('#selectAllIllumina').prop('checked', false);
-    }
-    if(affymetrix == total_affymetrix) {
-        $('#selectAllAffymetrix').prop('checked', true);
-    } else {
-        $('#selectAllAffymetrix').prop('checked', false);
-    }
-
-    if(illumina == total_illumina && affymetrix == total_affymetrix) {
-        $('#selectAllChipTypes').text("unselect all");
-    } else {
-        $('#selectAllChipTypes').text("select all");
-    }
-
+	//Determin if the master checkbox should be checked or not.
+	var illumina = $('.illumina:checked').length;
+	var affymetrix = $('.affymetrix:checked').length;
+	var total_illumina = $('input.illumina').length;
+	var total_affymetrix = $('input.affymetrix').length;
+
+	if (illumina == total_illumina) {
+		$('#selectAllIllumina').prop('checked', true);
+	} else {
+		$('#selectAllIllumina').prop('checked', false);
+	}
+	if (affymetrix == total_affymetrix) {
+		$('#selectAllAffymetrix').prop('checked', true);
+	} else {
+		$('#selectAllAffymetrix').prop('checked', false);
+	}
+
+	if (illumina == total_illumina && affymetrix == total_affymetrix) {
+		$('#selectAllChipTypes').text('unselect all');
+	} else {
+		$('#selectAllChipTypes').text('select all');
+	}
 }
 
 function toggleShowThinnedLists(toggleGlyph, listContainer) {
-    $('#' + toggleGlyph).on('click', function(e) {
-        if ($('#' + toggleGlyph).hasClass('glyphicon-plus')) {
-            $('#' + listContainer).show();
-        }
-        if ($('#' + toggleGlyph).hasClass('glyphicon-minus')) {
-            $('#' + listContainer).hide();
-        }
-        $('#' + toggleGlyph).toggleClass('glyphicon-minus glyphicon-plus');
-    });
+	$('#' + toggleGlyph).on('click', function (e) {
+		if ($('#' + toggleGlyph).hasClass('glyphicon-plus')) {
+			$('#' + listContainer).show();
+		}
+		if ($('#' + toggleGlyph).hasClass('glyphicon-minus')) {
+			$('#' + listContainer).hide();
+		}
+		$('#' + toggleGlyph).toggleClass('glyphicon-minus glyphicon-plus');
+	});
 }
 
 function setupLDexpressControls() {
-    // toggle show/hide thinned lists
-    toggleShowThinnedLists('toggle-show-ldexpress-thin-snps', 'ldexpress-snp-list');
-    toggleShowThinnedLists('toggle-show-ldexpress-thin-genes', 'ldexpress-genes-list');
-    toggleShowThinnedLists('toggle-show-ldexpress-thin-tissues', 'ldexpress-tissues-list');
-
-    $('#ldexpress-query-warnings-button').click( function() {
-        $('#new-ldexpress_wrapper').hide();
-        loadLDexpressQueryWarnings(ldExpressRaw);
-        $('#ldexpress-initial-message').hide();
-    });
-    initExpressTissues();
+	// toggle show/hide thinned lists
+	toggleShowThinnedLists(
+		'toggle-show-ldexpress-thin-snps',
+		'ldexpress-snp-list'
+	);
+	toggleShowThinnedLists(
+		'toggle-show-ldexpress-thin-genes',
+		'ldexpress-genes-list'
+	);
+	toggleShowThinnedLists(
+		'toggle-show-ldexpress-thin-tissues',
+		'ldexpress-tissues-list'
+	);
+
+	$('#ldexpress-query-warnings-button').click(function () {
+		$('#new-ldexpress_wrapper').hide();
+		loadLDexpressQueryWarnings(ldExpressRaw);
+		$('#ldexpress-initial-message').hide();
+	});
+	initExpressTissues();
 }
 
 function setupLDtraitControls() {
-    $('#ldtrait-snp-list').on('click', "a", function(e) {
-        //console.log("clicking on link");
-        var rs_number = e.target.id;
-        $('#ldtrait-snp-list').show();
-        $('#ldtrait-initial-message').hide();
-        loadLDtraitDetails(ldTraitRaw, rs_number, ldTraitSort);
-        $('#new-ldtrait-query-warnings_wrapper').hide();
-        $('#ldtrait-initial-message').hide();
-    });
-    $('#ldtrait-query-warnings-button').click( function() {
-        $('#new-ldtrait_wrapper').hide();
-        loadLDtraitQueryWarnings(ldTraitRaw);
-        $('#ldtrait-initial-message').hide();
-    });
-    initTraitTimestamp();
+	$('#ldtrait-snp-list').on('click', 'a', function (e) {
+		//console.log("clicking on link");
+		var rs_number = e.target.id;
+		$('#ldtrait-snp-list').show();
+		$('#ldtrait-initial-message').hide();
+		loadLDtraitDetails(ldTraitRaw, rs_number, ldTraitSort);
+		$('#new-ldtrait-query-warnings_wrapper').hide();
+		$('#ldtrait-initial-message').hide();
+	});
+	$('#ldtrait-query-warnings-button').click(function () {
+		$('#new-ldtrait_wrapper').hide();
+		loadLDtraitQueryWarnings(ldTraitRaw);
+		$('#ldtrait-initial-message').hide();
+	});
+	initTraitTimestamp();
 }
 
 function calculateChipTotals() {
+	var illumina = $('.illumina:checked').length;
+	var affymetrix = $('.affymetrix:checked').length;
 
-    var illumina = $(".illumina:checked").length;
-    var affymetrix = $(".affymetrix:checked").length;
-
-    $('#illumina-count').text(illumina);
-    $('#affymetrix-count').text(affymetrix);
-    if(illumina == 0 && affymetrix == 0) {
-        $("#snpchip").prop('disabled', true);
-    } else {
-        $("#snpchip").prop('disabled', false);
-    }
-
+	$('#illumina-count').text(illumina);
+	$('#affymetrix-count').text(affymetrix);
+	if (illumina == 0 && affymetrix == 0) {
+		$('#snpchip').prop('disabled', true);
+	} else {
+		$('#snpchip').prop('disabled', false);
+	}
 }
 
 function setupSNPclipControls() {
-    //('#snpclip').attr('disabled', false); // Remove this. (only need for testing)
-    $('#snpclip-snp-list').on('click', "a", function(e) {
-        //console.log("clicking on link");
-        var rs_number = e.target.id;
-        $('#snpclip-snp-list').show();
-        $('#snpclip-initial-message').hide();
-        loadSNPdetails(ldClipRaw, rs_number);
-        $('#snpclip-details').show();
-        $('#snpclip-warnings').hide();
-        $('#snpclip-initial-message').hide();
-    });
-    $('#snpclip-warnings-button').click( function() {
-        $('#snpclip-details').hide();
-        $('#snpclip-initial-message').hide();
-        $('#snpclip-warnings').show();
-    });
+	//('#snpclip').attr('disabled', false); // Remove this. (only need for testing)
+	$('#snpclip-snp-list').on('click', 'a', function (e) {
+		//console.log("clicking on link");
+		var rs_number = e.target.id;
+		$('#snpclip-snp-list').show();
+		$('#snpclip-initial-message').hide();
+		loadSNPdetails(ldClipRaw, rs_number);
+		$('#snpclip-details').show();
+		$('#snpclip-warnings').hide();
+		$('#snpclip-initial-message').hide();
+	});
+	$('#snpclip-warnings-button').click(function () {
+		$('#snpclip-details').hide();
+		$('#snpclip-initial-message').hide();
+		$('#snpclip-warnings').show();
+	});
 }
 
 /*
@@ -1415,18 +2163,18 @@ function pushInputs(currentTab, inputs) {
 */
 
 function showFFWarning() {
-    // Is this a version of Mozilla?
-    if ($.browser.mozilla) {
-        var userAgent = navigator.userAgent.toLowerCase();
-        // Is it Firefox?
-        if (userAgent.indexOf('firefox') != -1) {
-            userAgent = userAgent.substring(userAgent.indexOf('firefox/') + 8);
-            var version = userAgent.substring(0, userAgent.indexOf('.'));
-            if (version < 36) {
-                $('.ffWarning').show();
-            }
-        }
-    }
+	// Is this a version of Mozilla?
+	if ($.browser.mozilla) {
+		var userAgent = navigator.userAgent.toLowerCase();
+		// Is it Firefox?
+		if (userAgent.indexOf('firefox') != -1) {
+			userAgent = userAgent.substring(userAgent.indexOf('firefox/') + 8);
+			var version = userAgent.substring(0, userAgent.indexOf('.'));
+			if (version < 36) {
+				$('.ffWarning').show();
+			}
+		}
+	}
 }
 
 // Map knockout models to a sample json data
@@ -1436,409 +2184,454 @@ var snpclipModel = ko.mapping.fromJS(snpclipData);
 var snpchipModel = ko.mapping.fromJS(snpchipData);
 
 function RefreshTable(tableId, json) {
-    table = $(tableId).dataTable();
-    oSettings = table.fnSettings();
-    table.fnClearTable(this);
-    for (var i = 0; i < json.aaData.length; i++) {
-      table.oApi._fnAddData(oSettings, json.aaData[i]);
-    }
-    oSettings.aiDisplay = oSettings.aiDisplayMaster.slice();
-    table.fnDraw();
+	table = $(tableId).dataTable();
+	oSettings = table.fnSettings();
+	table.fnClearTable(this);
+	for (var i = 0; i < json.aaData.length; i++) {
+		table.oApi._fnAddData(oSettings, json.aaData[i]);
+	}
+	oSettings.aiDisplay = oSettings.aiDisplayMaster.slice();
+	table.fnDraw();
 }
 
 function RefreshTableSort(tableId, json, sort, r2Col, dCol) {
-    var sortCol;
-    if (sort == "r2") {
-        sortCol = r2Col;
-    } else {
-        sortCol = dCol;
-    }
-    table = $(tableId).dataTable();
-    oSettings = table.fnSettings();
-    table.fnSort([[sortCol, 'desc']]);
-    table.fnClearTable(this);
-    for (var i = 0; i < json.aaData.length; i++) {
-      table.oApi._fnAddData(oSettings, json.aaData[i]);
-    }
-    oSettings.aiDisplay = oSettings.aiDisplayMaster.slice();
-    table.fnDraw();
+	var sortCol;
+	if (sort == 'r2') {
+		sortCol = r2Col;
+	} else {
+		sortCol = dCol;
+	}
+	table = $(tableId).dataTable();
+	oSettings = table.fnSettings();
+	table.fnSort([[sortCol, 'desc']]);
+	table.fnClearTable(this);
+	for (var i = 0; i < json.aaData.length; i++) {
+		table.oApi._fnAddData(oSettings, json.aaData[i]);
+	}
+	oSettings.aiDisplay = oSettings.aiDisplayMaster.slice();
+	table.fnDraw();
 }
 
 function ldproxy_rs_results_link(data, type, row) {
-
-    //if no rs number is available return without a link.
-    if(!data.includes("rs") || data.length <= 2) {
-        return ".";
-    }
-    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
-    var rs_number = data.substring(2);
-    var params = {
-        rs : rs_number
-    };
-    //var href = server + "?" + $.param(params);
-    var href = server  + data;
-    var target = 'rs_number_' + Math.floor(Math.random() * (99999 - 10000 + 1));
-//  var href = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=128';
-    var link;
-    link = '<a href="'+href+'" target="'+target+'">'+data+'</a>';
-    //return data +' ('+ row[3]+')';
-    return link;
+	//if no rs number is available return without a link.
+	if (!data.includes('rs') || data.length <= 2) {
+		return '.';
+	}
+	var server = 'http://www.ncbi.nlm.nih.gov/snp/';
+	var rs_number = data.substring(2);
+	var params = {
+		rs: rs_number,
+	};
+	//var href = server + "?" + $.param(params);
+	var href = server + data;
+	var target = 'rs_number_' + Math.floor(Math.random() * (99999 - 10000 + 1));
+	//  var href = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=128';
+	var link;
+	link = '<a href="' + href + '" target="' + target + '">' + data + '</a>';
+	//return data +' ('+ row[3]+')';
+	return link;
 }
 
 function ldpop_ldpair_results_link(data, type, row, genomeBuild) {
-    // parse data
-    var snp1 = data[0];
-    var snp2 = data[1];
-    var pops = data[2];
-    var server = window.location.origin + '/?tab=ldpair';
-    var params = {
-        var1: snp1,
-        var2: snp2,
-        pop: pops,
-        genome_build: genomeBuild
-    };
-    var href = server + '&' + $.param(params);
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
-    return link;
+	// parse data
+	var snp1 = data[0];
+	var snp2 = data[1];
+	var pops = data[2];
+	var server = window.location.origin + '/?tab=ldpair';
+	var params = {
+		var1: snp1,
+		var2: snp2,
+		pop: pops,
+		genome_build: genomeBuild,
+	};
+	var href = server + '&' + $.param(params);
+	var link =
+		'<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
+	return link;
 }
 
 function ldexpress_gwas_catalog_link(data, type, row) {
-    var rsid = data;
-    var href = 'https://www.ebi.ac.uk/gwas/variants/' + rsid;
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
-    return link;
+	var rsid = data;
+	var href = 'https://www.ebi.ac.uk/gwas/variants/' + rsid;
+	var link =
+		'<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
+	return link;
 }
 
 function ldtrait_ldpair_results_link(snp1, snp2, pops, data) {
-    var server = window.location.origin + '/?tab=ldpair';
-    var params = {
-        var1: snp1,
-        var2: snp2,
-        pop: pops
-    };
-    var href = server + '&' + $.param(params);
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + ldtrait_parse_float(data).toString() + '</a>';
-    return link;
+	var server = window.location.origin + '/?tab=ldpair';
+	var params = {
+		var1: snp1,
+		var2: snp2,
+		pop: pops,
+	};
+	var href = server + '&' + $.param(params);
+	var link =
+		'<a style="color: #318fe2" href="' +
+		href +
+		'" + target="_blank">' +
+		ldtrait_parse_float(data).toString() +
+		'</a>';
+	return link;
 }
 
 function ldtrait_parse_float(data) {
-    // Round floats to 4 decimal places 
-    if (typeof data === 'string' || data instanceof String) {
-        return data;
-    } else {
-        if (parseFloat(data) == 1.0) {
-            return "1.0";
-        } else if (parseFloat(data) == 0.0) {
-            return "0.0";
-        } else if (parseFloat(data) <= 0.0001) {
-            return "<0.0001"
-        } else {
-            return parseFloat(data).toFixed(3);
-        }
-    }
+	// Round floats to 4 decimal places
+	if (typeof data === 'string' || data instanceof String) {
+		return data;
+	} else {
+		if (parseFloat(data) == 1.0) {
+			return '1.0';
+		} else if (parseFloat(data) == 0.0) {
+			return '0.0';
+		} else if (parseFloat(data) <= 0.0001) {
+			return '<0.0001';
+		} else {
+			return parseFloat(data).toFixed(3);
+		}
+	}
 }
 
 function ldexpress_Gencode_link(data, type, row) {
-    var href = 'https://ensembl.org/Homo_sapiens/Gene/Summary?g=' + data.split(".")[0];
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + data + '</a>';
-    return link;
+	var href =
+		'https://ensembl.org/Homo_sapiens/Gene/Summary?g=' + data.split('.')[0];
+	var link =
+		'<a style="color: #318fe2" href="' +
+		href +
+		'" + target="_blank">' +
+		data +
+		'</a>';
+	return link;
 }
 
 function ldexpress_NCBI_link(data, type, row) {
-    if (data.split("__")[1] === "NA") {
-        return data.split("__")[0];
-    } else {
-        var href = 'https://www.ncbi.nlm.nih.gov/gene/' + data.split("__")[1];
-        var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + data.split("__")[0] + '</a>';
-        return link;
-    }
+	if (data.split('__')[1] === 'NA') {
+		return data.split('__')[0];
+	} else {
+		var href = 'https://www.ncbi.nlm.nih.gov/gene/' + data.split('__')[1];
+		var link =
+			'<a style="color: #318fe2" href="' +
+			href +
+			'" + target="_blank">' +
+			data.split('__')[0] +
+			'</a>';
+		return link;
+	}
 }
 
 function ldexpress_GTEx_tissue_link(data, type, row) {
-    var href = 'https://www.gtexportal.org/home/eqtls/tissue?tissueName=' + data.split("__")[1];
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + data.split("__")[0] + '</a>';
-    return link;
+	var href =
+		'https://www.gtexportal.org/home/eqtls/tissue?tissueName=' +
+		data.split('__')[1];
+	var link =
+		'<a style="color: #318fe2" href="' +
+		href +
+		'" + target="_blank">' +
+		data.split('__')[0] +
+		'</a>';
+	return link;
 }
 
 function ldexpress_dbsnp_link(data, type, row) {
-    if (data.includes("rs")) {
-        var href = 'https://www.ncbi.nlm.nih.gov/snp/' + data;
-        var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + data + '</a>';
-        return link;
-    } else {
-        return data;
-    }
+	if (data.includes('rs')) {
+		var href = 'https://www.ncbi.nlm.nih.gov/snp/' + data;
+		var link =
+			'<a style="color: #318fe2" href="' +
+			href +
+			'" + target="_blank">' +
+			data +
+			'</a>';
+		return link;
+	} else {
+		return data;
+	}
 }
 
 function ldexpress_GTEx_effect_size_link(data, type, row) {
-    // Round floats to 3 decimal places if string can be parsed to float
-    if (!isNaN(parseFloat(data.split("__")[0]))) {
-        var display = parseFloat(data.split("__")[0]).toFixed(3);
-    } else {
-        var display = data.split("__")[0];
-    }
-    var href = 'https://www.gtexportal.org/home/snp/' + data.split("__")[1];
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + display + '</a>';
-    return link;
+	// Round floats to 3 decimal places if string can be parsed to float
+	if (!isNaN(parseFloat(data.split('__')[0]))) {
+		var display = parseFloat(data.split('__')[0]).toFixed(3);
+	} else {
+		var display = data.split('__')[0];
+	}
+	var href = 'https://www.gtexportal.org/home/snp/' + data.split('__')[1];
+	var link =
+		'<a style="color: #318fe2" href="' +
+		href +
+		'" + target="_blank">' +
+		display +
+		'</a>';
+	return link;
 }
 
 function ldexpress_GTEx_pvalue_link(data, type, row) {
-    // Round floats to 4 decimal places 
-    if (type === 'display') {
-        var floatData  = parseFloat(data.split("__")[0]);
-        if (data.split("__")[0] != "NA" && floatData) {
-            if (floatData === 1.0) {
-                var display = "1.0";
-            } else if (floatData === 0.0) {
-                var display = "0.0";
-            } else {
-                var val = floatData.toExponential(0).split(/E/i);
-                var display = val[0] + "x10" + val[1].sup();
-            }
-        } else {
-            if (floatData === 0.0 && (data.split("__")[0].includes("E") || data.split("__")[0].includes("e"))) {
-                var val = data.split("__")[0].split(/E/i);
-                var display = val[0] + "x10" + val[1].sup();
-            } else {
-                var display = data.split("__")[0];
-            }
-        }
-    } else {
-        var display = data.split("__")[0];
-    }
-    var href = 'https://www.gtexportal.org/home/snp/' + data.split("__")[1];
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">' + display + '</a>';
-    return link;
+	// Round floats to 4 decimal places
+	if (type === 'display') {
+		var floatData = parseFloat(data.split('__')[0]);
+		if (data.split('__')[0] != 'NA' && floatData) {
+			if (floatData === 1.0) {
+				var display = '1.0';
+			} else if (floatData === 0.0) {
+				var display = '0.0';
+			} else {
+				var val = floatData.toExponential(0).split(/E/i);
+				var display = val[0] + 'x10' + val[1].sup();
+			}
+		} else {
+			if (
+				floatData === 0.0 &&
+				(data.split('__')[0].includes('E') || data.split('__')[0].includes('e'))
+			) {
+				var val = data.split('__')[0].split(/E/i);
+				var display = val[0] + 'x10' + val[1].sup();
+			} else {
+				var display = data.split('__')[0];
+			}
+		}
+	} else {
+		var display = data.split('__')[0];
+	}
+	var href = 'https://www.gtexportal.org/home/snp/' + data.split('__')[1];
+	var link =
+		'<a style="color: #318fe2" href="' +
+		href +
+		'" + target="_blank">' +
+		display +
+		'</a>';
+	return link;
 }
 
 function ldtrait_gwas_catalog_link(data, type, row) {
-    var rsid = data;
-    var href = 'https://www.ebi.ac.uk/gwas/variants/' + rsid;
-    var link = '<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
-    return link;
+	var rsid = data;
+	var href = 'https://www.ebi.ac.uk/gwas/variants/' + rsid;
+	var link =
+		'<a style="color: #318fe2" href="' + href + '" + target="_blank">link</a>';
+	return link;
 }
 
 function ldproxy_position_link(data, type, row) {
-
-    // Find the coord of the rs number
-    //
-    // Cluster Report:
-    //
-    var server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
-    // https://genome.ucsc.edu/cgi-bin/hgTracks?
-    // position=chr4:103554686-104554686
-    // &snp141=pack
-    // &hgFind.matches=rs2720460
-    // snp1-coord
-
-    //
-    // Genome Browser:
-    //
-
-    //var positions = data.query_snp.Coord.split(":");
-    //Example:
-    //http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7%3A24958727-24959227&snp141=pack&hgFind.matches=rs128
-    var chr = row[1];
-    var mid_value = parseInt(data);
-    var offset = 250;
-    var range = (mid_value - offset) + "-" + (mid_value + offset);
-    var position = chr + ":" + range;
-    var rs_number = row[0];
-    var params = {
-        db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
-        position : position,
-        snp151 : 'pack',
-        'hgFind.matches' : rs_number
-    };
-    var href = server + "?" + $.param(params);
-    var target = 'position_' + Math.floor(Math.random() * (99999 - 10000 + 1));
-    var link = '<a href="'+href+'" target="'+target+'">'+data+'</a>';
-
-    return link;
+	// Find the coord of the rs number
+	//
+	// Cluster Report:
+	//
+	var server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
+	// https://genome.ucsc.edu/cgi-bin/hgTracks?
+	// position=chr4:103554686-104554686
+	// &snp141=pack
+	// &hgFind.matches=rs2720460
+	// snp1-coord
+
+	//
+	// Genome Browser:
+	//
+
+	//var positions = data.query_snp.Coord.split(":");
+	//Example:
+	//http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7%3A24958727-24959227&snp141=pack&hgFind.matches=rs128
+	var chr = row[1];
+	var mid_value = parseInt(data);
+	var offset = 250;
+	var range = mid_value - offset + '-' + (mid_value + offset);
+	var position = chr + ':' + range;
+	var rs_number = row[0];
+	var params = {
+		db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
+		position: position,
+		snp151: 'pack',
+		'hgFind.matches': rs_number,
+	};
+	var href = server + '?' + $.param(params);
+	var target = 'position_' + Math.floor(Math.random() * (99999 - 10000 + 1));
+	var link = '<a href="' + href + '" target="' + target + '">' + data + '</a>';
+
+	return link;
 }
 
 function ldproxy_regulome_link(data, type, row) {
-    // Create RegulomeDB links
-    var server = 'https://www.regulomedb.org/regulome-search';
-    var chr = row[1];
-    var mid_value = parseInt(row[2]);
-    var zero_base = mid_value - 1;
-    var params = {
-        genome: genomeBuild == "grch37" ? "GRCh37" : "GRCh38",
-        regions : chr + ":" + zero_base + "-" + mid_value
-    }
-    var href = server + "?" + $.param(params);
-    var link = '<a href="' + href + '" target="_blank">' + data + '</a>';
-    return link;
+	// Create RegulomeDB links
+	var server = 'https://www.regulomedb.org/regulome-search';
+	var chr = row[1];
+	var mid_value = parseInt(row[2]);
+	var zero_base = mid_value - 1;
+	var params = {
+		genome: genomeBuild == 'grch37' ? 'GRCh37' : 'GRCh38',
+		regions: chr + ':' + zero_base + '-' + mid_value,
+	};
+	var href = server + '?' + $.param(params);
+	var link = '<a href="' + href + '" target="_blank">' + data + '</a>';
+	return link;
 }
 
-
 function ldproxy_haploreg_link(data, type, row) {
+	// Create RegulomeDB links
 
-    // Create RegulomeDB links
-
-    var server = 'http://pubs.broadinstitute.org/mammals/haploreg/detail_v4.1.php';
+	var server =
+		'http://pubs.broadinstitute.org/mammals/haploreg/detail_v4.1.php';
 
-    var rs_number = row[0];
-    var params = {
-        query : "",
-        id : rs_number
-    };
-    var href = server + "?" + $.param(params);
-    var target = 'haploreg_' + Math.floor(Math.random() * (99999 - 10000 + 1));
-    var img = '<img src="LDproxy_external_link.png" alt="HaploReg Details" title="HaploReg Details" class="haploreg_external_link" style="width:16px;height:16px;">';
-    var link = '<a href="'+href+'" target="'+target+'">'+img+'</a>';
-
-    return link;
+	var rs_number = row[0];
+	var params = {
+		query: '',
+		id: rs_number,
+	};
+	var href = server + '?' + $.param(params);
+	var target = 'haploreg_' + Math.floor(Math.random() * (99999 - 10000 + 1));
+	var img =
+		'<img src="LDproxy_external_link.png" alt="HaploReg Details" title="HaploReg Details" class="haploreg_external_link" style="width:16px;height:16px;">';
+	var link = '<a href="' + href + '" target="' + target + '">' + img + '</a>';
 
+	return link;
 }
 
 function ldproxy_FORGEdb_link(data, type, row) {
+	// Create FORGEDB links
 
-    // Create FORGEDB links
-
-    var server = 'https://forge2.altiusinstitute.org/files/';
+	var server = 'https://forge2.altiusinstitute.org/files/';
 
-    var snp = row[0];
-    var score = row[9];
-    
-    var href = server + snp.substring(0,6) + "/summary.table."+ snp + ".html"
-    //var img = '<img src="LDproxy_external_link.png" alt=FORGEdb Details" title="FORGEdb Details" class="haploreg_external_link" style="width:16px;height:16px;">';
-    var link = '<a href="' + href + '" target="_blank">'+score+'</a>';
+	var snp = row[0];
+	var score = row[9];
 
-    return link;
+	var href = server + snp.substring(0, 6) + '/summary.table.' + snp + '.html';
+	//var img = '<img src="LDproxy_external_link.png" alt=FORGEdb Details" title="FORGEdb Details" class="haploreg_external_link" style="width:16px;height:16px;">';
+	var link = '<a href="' + href + '" target="_blank">' + score + '</a>';
 
+	return link;
 }
 
 function ldassoc_FORGEdb_link(data, type, row) {
+	// Create FORGEDB links
 
-    // Create FORGEDB links
+	var server = 'https://forge2.altiusinstitute.org/files/';
 
-    var server = 'https://forge2.altiusinstitute.org/files/';
+	var snp = row[0];
+	var score = row[10];
 
-    var snp = row[0];
-    var score = row[10];
-    
-    var href = server + snp.substring(0,6) + "/summary.table."+ snp + ".html"
-    //var img = '<img src="LDproxy_external_link.png" alt=FORGEdb Details" title="FORGEdb Details" class="haploreg_external_link" style="width:16px;height:16px;">';
-    var link = '<a href="' + href + '" target="_blank">'+score+'</a>';
-
-    return link;
+	var href = server + snp.substring(0, 6) + '/summary.table.' + snp + '.html';
+	//var img = '<img src="LDproxy_external_link.png" alt=FORGEdb Details" title="FORGEdb Details" class="haploreg_external_link" style="width:16px;height:16px;">';
+	var link = '<a href="' + href + '" target="_blank">' + score + '</a>';
 
+	return link;
 }
 
 function updateVersion(version) {
-    $("#ldlink_version").text(version);
+	$('#ldlink_version').text(version);
 }
 
 function cleanSNP(text) {
-    //
-    //Clean up file remove spaces.
-    //  Only allow first column
-    //
-    var lines = text.split('\n');
-    var list = "";
-    var variant = "";
-
-    $.each(lines, function (key, value) {
-        var clean = value.replace(/\t/, " ");
-        var line = clean.replace(/[^[A-Z0-9\n \:]/ig, "");
-        line = line.split(' ');
-        variant = "";
-        $.each(line, function(key,value){
-            if(value != "") {
-                variant = value;
-                return false;
-            }
-        });
-
-        if(variant.length > 2) {
-            // var pos = variant.search(/^[R|r][S|s]\d+$/);
-            // add genomic positions too (ex. chr1:123456) in the future
-            var pos = variant.search(/^(([ |\t])*[r|R][s|S]\d+([ |\t])*|([ |\t])*[c|C][h|H][r|R][\d|x|X|y|Y]\d?:\d+([ |\t])*)$/);
-            if(pos == 0) {
-                list += variant + '\n';
-            }
-        }
-    });
-    return list;
+	//
+	//Clean up file remove spaces.
+	//  Only allow first column
+	//
+	var lines = text.split('\n');
+	var list = '';
+	var variant = '';
+
+	$.each(lines, function (key, value) {
+		var clean = value.replace(/\t/, ' ');
+		var line = clean.replace(/[^[A-Z0-9\n \:]/gi, '');
+		line = line.split(' ');
+		variant = '';
+		$.each(line, function (key, value) {
+			if (value != '') {
+				variant = value;
+				return false;
+			}
+		});
+
+		if (variant.length > 2) {
+			// var pos = variant.search(/^[R|r][S|s]\d+$/);
+			// add genomic positions too (ex. chr1:123456) in the future
+			var pos = variant.search(
+				/^(([ |\t])*[r|R][s|S]\d+([ |\t])*|([ |\t])*[c|C][h|H][r|R][\d|x|X|y|Y]\d?:\d+([ |\t])*)$/
+			);
+			if (pos == 0) {
+				list += variant + '\n';
+			}
+		}
+	});
+	return list;
 }
 
 function populateTextArea(event, numFiles, label) {
-    id = event.target.id;
-    if (window.FileReader) {
-
-        var input = event.target;
-        var reader = new FileReader();
-        reader.onload = function() {
-            var text = reader.result;
-            $('#'+id+'-snp-numbers').val(cleanSNP(text));
-            $('#'+id+'-snp-numbers').keyup();
-        };
-        reader.readAsText(input.files[0]);
-    } else {
-        alert('FileReader not supported');
-        return;
-    }
+	id = event.target.id;
+	if (window.FileReader) {
+		var input = event.target;
+		var reader = new FileReader();
+		reader.onload = function () {
+			var text = reader.result;
+			$('#' + id + '-snp-numbers').val(cleanSNP(text));
+			$('#' + id + '-snp-numbers').keyup();
+		};
+		reader.readAsText(input.files[0]);
+	} else {
+		alert('FileReader not supported');
+		return;
+	}
 }
 
 function populateAssocDropDown(headers) {
-    $.each(dropdowns, function(i, id) {
-        $("#"+id).find("ul").empty();
-        $.each(headers, function(key, value){
-            $("#"+id).find("ul").append('<li role="presentation"><a role="menuitem" tabindex="-1">'+value+'</a></li>');
-        });
-        var previous_value = readCookie(id);
-        //console.log("You previous selected: "+previous_value);
-        if($.inArray(previous_value, headers) != -1) {
-            setBootstrapSelector(id, previous_value);
-        } else {
-            resetBootstrapSelector(id);
-        }
-    });
+	$.each(dropdowns, function (i, id) {
+		$('#' + id)
+			.find('ul')
+			.empty();
+		$.each(headers, function (key, value) {
+			$('#' + id)
+				.find('ul')
+				.append(
+					'<li role="presentation"><a role="menuitem" tabindex="-1">' +
+						value +
+						'</a></li>'
+				);
+		});
+		var previous_value = readCookie(id);
+		//console.log("You previous selected: "+previous_value);
+		if ($.inArray(previous_value, headers) != -1) {
+			setBootstrapSelector(id, previous_value);
+		} else {
+			resetBootstrapSelector(id);
+		}
+	});
 }
 
 function parseHeaderValues(header_line) {
-    //alert(header_line);
-    //Assumption: No spaces in the header title for each column.  Either a space or comma between header titles.
-    var clean = header_line.replace(/\t/g, " ");
-    clean = clean.replace(/","/g, " ");
-    clean = clean.replace(/,/g, " ");
-    //var line = clean.replace(/[^[A-Z0-9\n ]/ig, "");
-    //console.log("Here is clean");
-    //console.log(clean);
-    var headers = clean.split(" ");
-    //console.log(headers);
-    var new_headers = headers.filter(function(v){return v!==''});
-    //console.log(new_headers);
-
-    populateAssocDropDown(new_headers);
-
+	//alert(header_line);
+	//Assumption: No spaces in the header title for each column.  Either a space or comma between header titles.
+	var clean = header_line.replace(/\t/g, ' ');
+	clean = clean.replace(/","/g, ' ');
+	clean = clean.replace(/,/g, ' ');
+	//var line = clean.replace(/[^[A-Z0-9\n ]/ig, "");
+	//console.log("Here is clean");
+	//console.log(clean);
+	var headers = clean.split(' ');
+	//console.log(headers);
+	var new_headers = headers.filter(function (v) {
+		return v !== '';
+	});
+	//console.log(new_headers);
+
+	populateAssocDropDown(new_headers);
 }
 
 function getHeaderLine(header) {
-    //console.log(header);
-    var index = 0;
-    //var view = new Uint8Array(header);
-    var view = header;
-    for(index=0;index<=header.length;index++) {
-        if (header.charCodeAt(index) === 10 || header.charCodeAt(index) === 13) {
-            //console.log("Found a return");
-            parseHeaderValues(header.substr(0, index));
-            return;
-        }
-    }
-
-    //console.warn("Did not find a return in the header line. Please fix input file.  Make sure the header line is the first line and has a return.");
+	//console.log(header);
+	var index = 0;
+	//var view = new Uint8Array(header);
+	var view = header;
+	for (index = 0; index <= header.length; index++) {
+		if (header.charCodeAt(index) === 10 || header.charCodeAt(index) === 13) {
+			//console.log("Found a return");
+			parseHeaderValues(header.substr(0, index));
+			return;
+		}
+	}
 
+	//console.warn("Did not find a return in the header line. Please fix input file.  Make sure the header line is the first line and has a return.");
 }
 
 function populateHeaderValues(event, numFiles, label) {
-
-    console.warn("populateHeaderValues");
-    //findColumnLength(event.target.files[0], printLength);
-    parseFile(event.target.files[0], getHeaderLine);
-    /*
+	console.warn('populateHeaderValues');
+	//findColumnLength(event.target.files[0], printLength);
+	parseFile(event.target.files[0], getHeaderLine);
+	/*
     id = event.target.id;
     if (window.FileReader) {
 
@@ -1858,1279 +2651,1420 @@ function populateHeaderValues(event, numFiles, label) {
 }
 
 function loadHelp() {
-    $('#help-tab').load('help.html?v=5.6.0');
+	$('#help-tab').load('help.html?v=5.6.0');
 }
 
 function calculate(e) {
-    var formId = e.target.id;
-    e.preventDefault();
+	var formId = e.target.id;
+	e.preventDefault();
 
-    // strip out "Form" from id
-    var id = formId.slice(0, formId.length - 4);
-
-    initCalculate(id);
-    updateData(id);
+	// strip out "Form" from id
+	var id = formId.slice(0, formId.length - 4);
 
+	initCalculate(id);
+	updateData(id);
 }
 
 function initCalculate(id) {
-    $('#'+id+'-results-container').hide();
-    $('#'+id+'-message').hide();
-    $('#'+id+'-message-warning').hide();
+	$('#' + id + '-results-container').hide();
+	$('#' + id + '-message').hide();
+	$('#' + id + '-message-warning').hide();
 }
 
 function updateData(id) {
-
-    switch (id) {
-        case 'ldassoc':
-            if(isBrowseSet(id) && isRegionSet(id) && areRegionDetailsSet(id) && isPopulationSet(id)) {
-                $('#'+id+"-loading").show();
-                updateLDassoc();
-            }
-            break;
-        case 'ldexpress':
-            if(isPopulationSet(id) && isTissueSet(id) && validateLDexpressBasePairWindow()) {
-                $('#'+id+"-loading").show();
-                updateLDexpress();
-            }
-            break;
-        case 'ldhap':
-            if(isPopulationSet(id)) {
-                $('#'+id+"-loading").show();
-                updateLDhap();
-            }
-            break;
-        case 'ldmatrix':
-            if(isPopulationSet(id) && checkSNPListLength(id)) {
-                $('#'+id+"-loading").show();
-                updateLDmatrix();
-            }
-            break;
-        case 'ldpair':
-            if(isPopulationSet(id)) {
-                $('#'+id+"-loading").show();
-                updateLDpair();
-            }
-            break;
-        case 'ldpop':
-            if(isPopulationSet(id)) {
-                $('#'+id+"-loading").show();
-                updateLDpop();
-            }
-            break;
-        case 'ldproxy':
-            if(isPopulationSet(id) && validateLDproxyBasePairWindow()) {
-                $('#'+id+"-loading").show();
-                updateLDproxy();
-            }
-            break;
-        case 'ldtrait':
-            if(isPopulationSet(id) && validateLDtraitBasePairWindow()) {
-                $('#'+id+"-loading").show();
-                updateLDtrait();
-            }
-            break;
-        case 'snpclip':
-            if(isPopulationSet(id)) {
-                $('#'+id+"-loading").show();
-                updateSNPclip();
-            }
-            break;
-        case 'snpchip':
-            $('#'+id+"-loading").show();
-            updateSNPchip();
-            break;
-        case 'apiaccess':
-            $('#'+id+"-loading").show();
-            updateAPIaccess();
-            break;
-        case 'apiblocked':
-            if(checkTextAreaLength(id)) {
-                $('#'+id+"-loading").show();
-                updateAPIblocked();
-                break;
-            }
-    }
+	switch (id) {
+		case 'ldassoc':
+			if (
+				isBrowseSet(id) &&
+				isRegionSet(id) &&
+				areRegionDetailsSet(id) &&
+				isPopulationSet(id)
+			) {
+				$('#' + id + '-loading').show();
+				updateLDassoc();
+			}
+			break;
+		case 'ldexpress':
+			if (
+				isPopulationSet(id) &&
+				isTissueSet(id) &&
+				validateLDexpressBasePairWindow()
+			) {
+				$('#' + id + '-loading').show();
+				updateLDexpress();
+			}
+			break;
+		case 'ldhap':
+			if (isPopulationSet(id)) {
+				$('#' + id + '-loading').show();
+				updateLDhap();
+			}
+			break;
+		case 'ldmatrix':
+			if (isPopulationSet(id) && checkSNPListLength(id)) {
+				$('#' + id + '-loading').show();
+				updateLDmatrix();
+			}
+			break;
+		case 'ldpair':
+			if (isPopulationSet(id)) {
+				$('#' + id + '-loading').show();
+				updateLDpair();
+			}
+			break;
+		case 'ldpop':
+			if (isPopulationSet(id)) {
+				$('#' + id + '-loading').show();
+				updateLDpop();
+			}
+			break;
+		case 'ldproxy':
+			if (isPopulationSet(id) && validateLDproxyBasePairWindow()) {
+				$('#' + id + '-loading').show();
+				updateLDproxy();
+			}
+			break;
+		case 'ldtrait':
+			if (isPopulationSet(id) && validateLDtraitBasePairWindow()) {
+				$('#' + id + '-loading').show();
+				updateLDtrait();
+			}
+			break;
+		case 'snpclip':
+			if (isPopulationSet(id)) {
+				$('#' + id + '-loading').show();
+				updateSNPclip();
+			}
+			break;
+		case 'snpchip':
+			$('#' + id + '-loading').show();
+			updateSNPchip();
+			break;
+		case 'apiaccess':
+			$('#' + id + '-loading').show();
+			updateAPIaccess();
+			break;
+		case 'apiblocked':
+			if (checkTextAreaLength(id)) {
+				$('#' + id + '-loading').show();
+				updateAPIblocked();
+				break;
+			}
+	}
 }
 
 function isBrowseSet(elementId) {
-    var query = $('#header-values');
-    var isVisible = query.is(':visible');
-    if(isVisible === true) {
-        $('#'+elementId+'-browse-set-none').popover('hide');
-        return true;
-    } else {
-        $('#'+elementId+'-browse-set-none').popover('show');
-        setTimeout(function() { $('#'+elementId+'-browse-set-none').popover('hide'); }, 4000);
-        return false;
-    }
+	var query = $('#header-values');
+	var isVisible = query.is(':visible');
+	if (isVisible === true) {
+		$('#' + elementId + '-browse-set-none').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-browse-set-none').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-browse-set-none').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isRegionSet(elementId) {
-    var region =  $('#region-codes-menu1').html().replace(/&nbsp;<span class="caret"><\/span>/, "");
-    if(region == "Gene" || region == "Region" || region == "Variant") {
-        $('#'+elementId+'-region-codes-zero').popover('hide');
-        return true;
-    } else {
-        $('#'+elementId+'-region-codes-zero').popover('show');
-        setTimeout(function() { $('#'+elementId+'-region-codes-zero').popover('hide'); }, 4000);
-        return false;
-    }
+	var region = $('#region-codes-menu1')
+		.html()
+		.replace(/&nbsp;<span class="caret"><\/span>/, '');
+	if (region == 'Gene' || region == 'Region' || region == 'Variant') {
+		$('#' + elementId + '-region-codes-zero').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-region-codes-zero').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-region-codes-zero').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isGeneNameSet(elementId) {
-  if ($('#region-gene-name').val().toString().length > 0) {
-    $('#'+elementId+'-region-gene-name').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-region-gene-name').popover('show');
-    setTimeout(function() { $('#'+elementId+'-region-gene-name').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-gene-name').val().toString().length > 0) {
+		$('#' + elementId + '-region-gene-name').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-region-gene-name').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-region-gene-name').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isGeneBPSet(elementId) {
-  if ($('#region-gene-base-pair-window').val().toString().length > 0) {
-    $('#'+elementId+'-region-gene-bp').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-region-gene-bp').popover('show');
-    setTimeout(function() { $('#'+elementId+'-region-gene-bp').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-gene-base-pair-window').val().toString().length > 0) {
+		$('#' + elementId + '-region-gene-bp').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-region-gene-bp').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-region-gene-bp').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isRegionStartSet(elementId) {
-  if ($('#region-region-start-coord').val().toString().length > 0) {
-    $('#'+elementId+'-region-region-start').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-region-region-start').popover('show');
-    setTimeout(function() { $('#'+elementId+'-region-region-start').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-region-start-coord').val().toString().length > 0) {
+		$('#' + elementId + '-region-region-start').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-region-region-start').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-region-region-start').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isRegionEndSet(elementId) {
-  if ($('#region-region-end-coord').val().toString().length > 0) {
-    $('#'+elementId+'-region-region-end').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-region-region-end').popover('show');
-    setTimeout(function() { $('#'+elementId+'-region-region-end').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-region-end-coord').val().toString().length > 0) {
+		$('#' + elementId + '-region-region-end').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-region-region-end').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-region-region-end').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isVariantIndexSet(elementId) {
-  if ($('#region-variant-index').val().toString().length > 0) {
-    $('#'+elementId+'-variant-index-pop').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-variant-index-pop').popover('show');
-    setTimeout(function() { $('#'+elementId+'-variant-index-pop').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-variant-index').val().toString().length > 0) {
+		$('#' + elementId + '-variant-index-pop').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-variant-index-pop').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-variant-index-pop').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function isVariantBPSet(elementId) {
-  if ($('#region-variant-base-pair-window').val().toString().length > 0) {
-    $('#'+elementId+'-variant-bp-pop').popover('hide');
-    return true;
-  }
-  else {
-    $('#'+elementId+'-variant-bp-pop').popover('show');
-    setTimeout(function() { $('#'+elementId+'-variant-bp-pop').popover('hide'); }, 4000);
-    return false;
-  }
+	if ($('#region-variant-base-pair-window').val().toString().length > 0) {
+		$('#' + elementId + '-variant-bp-pop').popover('hide');
+		return true;
+	} else {
+		$('#' + elementId + '-variant-bp-pop').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-variant-bp-pop').popover('hide');
+		}, 4000);
+		return false;
+	}
 }
 
 function areRegionDetailsSet(elementId) {
-    var region =  $('#region-codes-menu1').html().replace(/&nbsp;<span class="caret"><\/span>/, "");
-    if (region == "Gene") {
-      // gene name
-      // bp window
-      if (isGeneNameSet(elementId) && isGeneBPSet(elementId)) {
-        return true;
-      }
-      else {
-        return false;
-      }
-    }
-    if (region == "Region") {
-      // region start
-      // region end
-      if (isRegionStartSet(elementId) && isRegionEndSet(elementId)) {
-        return true;
-      }
-      else {
-        return false;
-      }
-    }
-    if (region == "Variant") {
-      // index variant
-      // bp window
-      if (isVariantIndexSet(elementId) && isVariantBPSet(elementId)) {
-        return true;
-      }
-      else {
-        return false;
-      }
-    }
+	var region = $('#region-codes-menu1')
+		.html()
+		.replace(/&nbsp;<span class="caret"><\/span>/, '');
+	if (region == 'Gene') {
+		// gene name
+		// bp window
+		if (isGeneNameSet(elementId) && isGeneBPSet(elementId)) {
+			return true;
+		} else {
+			return false;
+		}
+	}
+	if (region == 'Region') {
+		// region start
+		// region end
+		if (isRegionStartSet(elementId) && isRegionEndSet(elementId)) {
+			return true;
+		} else {
+			return false;
+		}
+	}
+	if (region == 'Variant') {
+		// index variant
+		// bp window
+		if (isVariantIndexSet(elementId) && isVariantBPSet(elementId)) {
+			return true;
+		} else {
+			return false;
+		}
+	}
 }
 
 function isPopulationSet(elementId) {
-    var population =  $('#' + elementId + '-population-codes').val();
-    if(population == null ) {
-        $('#' + elementId + '-population-codes-zero').popover('show');
-        setTimeout(function() { $('#' + elementId + '-population-codes-zero').popover('hide'); }, 4000);
-        return false;
-    } else {
-        $('#' + elementId + '-population-codes-zero').popover('hide');
-        return true;
-    }
+	var population = $('#' + elementId + '-population-codes').val();
+	if (population == null) {
+		$('#' + elementId + '-population-codes-zero').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-population-codes-zero').popover('hide');
+		}, 4000);
+		return false;
+	} else {
+		$('#' + elementId + '-population-codes-zero').popover('hide');
+		return true;
+	}
 }
 
 function isTissueSet(elementId) {
-    var tissue =  $('#'+elementId+'-tissue-codes').val();
-    if(tissue == null ) {
-        $('#' + elementId + '-tissue-codes-zero').popover('show');
-        setTimeout(function() { $('#'+elementId+'-tissue-codes-zero').popover('hide'); }, 4000);
-        return false;
-    } else {
-        $('#'+elementId+'-tissue-codes-zero').popover('hide');
-        return true;
-    }
+	var tissue = $('#' + elementId + '-tissue-codes').val();
+	if (tissue == null) {
+		$('#' + elementId + '-tissue-codes-zero').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-tissue-codes-zero').popover('hide');
+		}, 4000);
+		return false;
+	} else {
+		$('#' + elementId + '-tissue-codes-zero').popover('hide');
+		return true;
+	}
 }
 
 function checkSNPListLength(elementId) {
-    var snps =  $('#'+elementId+'-file-snp-numbers').val();
-    var snplist = snps.split("\n");
-    // console.log(snplist);
-    snplist = snplist.filter(Boolean);
-    // console.log(snplist.length);
-    if(snplist.length > 300) {
-        $('#'+elementId+'-file-snp-warning').popover('show');
-        setTimeout(function() { $('#'+elementId+'-file-snp-warning').popover('hide'); }, 4000);
-        return false;
-    } else {
-        $('#'+elementId+'-file-snp-warning').popover('hide');
-        return true;
-    }
+	var snps = $('#' + elementId + '-file-snp-numbers').val();
+	var snplist = snps.split('\n');
+	// console.log(snplist);
+	snplist = snplist.filter(Boolean);
+	// console.log(snplist.length);
+	if (snplist.length > 300) {
+		$('#' + elementId + '-file-snp-warning').popover('show');
+		setTimeout(function () {
+			$('#' + elementId + '-file-snp-warning').popover('hide');
+		}, 4000);
+		return false;
+	} else {
+		$('#' + elementId + '-file-snp-warning').popover('hide');
+		return true;
+	}
 }
 
 function checkTextAreaLength(elementId) {
-    var description =  $('#'+elementId+'-justification').val();
-    var count = description.length;
-    if(count > 500 ) {
-        $('#'+elementId+'-justification-warning').popover('show');
-        var message = "Please keep response under 500 characters. Current: " + count.toString() + " characters."
-        $('#'+elementId+'-justification-warning').attr('data-content', message);
-        setTimeout(function() { $('#'+elementId+'-justification-warning').popover('hide'); }, 4000);
-        return false;
-    } else {
-        $('#'+elementId+'-justification-warning').popover('hide');
-        return true;
-    }
-    // minimum character count
-    // else if(count < 50) {
-    //     $('#'+elementId+'-justification-warning').popover('show');
-    //     var message = "Please respond with at least 50 characters. Current: " + count.toString() + " characters."
-    //     $('#'+elementId+'-justification-warning').attr('data-content', message);
-    //     setTimeout(function() { $('#'+elementId+'-justification-warning').popover('hide'); }, 4000);
-    //     return false;
-    // } 
+	var description = $('#' + elementId + '-justification').val();
+	var count = description.length;
+	if (count > 500) {
+		$('#' + elementId + '-justification-warning').popover('show');
+		var message =
+			'Please keep response under 500 characters. Current: ' +
+			count.toString() +
+			' characters.';
+		$('#' + elementId + '-justification-warning').attr('data-content', message);
+		setTimeout(function () {
+			$('#' + elementId + '-justification-warning').popover('hide');
+		}, 4000);
+		return false;
+	} else {
+		$('#' + elementId + '-justification-warning').popover('hide');
+		return true;
+	}
+	// minimum character count
+	// else if(count < 50) {
+	//     $('#'+elementId+'-justification-warning').popover('show');
+	//     var message = "Please respond with at least 50 characters. Current: " + count.toString() + " characters."
+	//     $('#'+elementId+'-justification-warning').attr('data-content', message);
+	//     setTimeout(function() { $('#'+elementId+'-justification-warning').popover('hide'); }, 4000);
+	//     return false;
+	// }
 }
-    
 
 function updateLDassoc() {
-
-    var id = "ldassoc";
-
-    var $btn = $('#' + id).button('loading');
-    var population = getPopulationCodes(id+'-population-codes');
-    var ldInputs = {
-        pop : population.join("+"),
-        filename : $("#ldassoc-file-label").val(),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        columns : new Object,
-        calculateRegion: $("#assoc-region > button").val(),
-        gene: new Object(),
-        region: new Object(),
-        variant: new Object(),
-        genome_build: genomeBuild,
-        dprime: $("#assoc-matrix-color-r2").hasClass('active') ? "False" :"True",
-        transcript: $("#assoc-transcript").hasClass('active') ? "False" :"True",
-        //annotate: $("#assoc-annotate").hasClass('active') ? "True" :"False",
-        //annotate: $("#assoc-annotate").val(),
-        annotate: document.querySelector('input[name="ldassoc_options"]:checked').value,
-        useEx: $('#example-gwas').is(':checked')? "True" :"False"
-    };
-
-
-    ldInputs.columns.chromosome = $("#assoc-chromosome > button").val();
-    ldInputs.columns.position = $("#assoc-position > button").val();
-    ldInputs.columns.pvalue = $("#assoc-p-value > button").val();
-    //gene
-    ldInputs.gene.name = $("#region-gene-name").val();
-    ldInputs.gene.basepair = $("#region-gene-base-pair-window").val();
-    ldInputs.gene.index = $("#region-gene-index").val();
-    //region
-    ldInputs.region.start = $("#region-region-start-coord").val();
-    ldInputs.region.end = $("#region-region-end-coord").val();
-    ldInputs.region.index = $("#region-region-index").val();
-    //variant
-    ldInputs.variant.index = $("#region-variant-index").val();
-    ldInputs.variant.basepair = $("#region-variant-base-pair-window").val();
-
-    var tempbuild = genomeBuild == 'grch37' ? 'hg19' : 'hg38'
-    var r2url = 'https://genome.ucsc.edu/cgi-bin/hgTracks?db=' + tempbuild  + '&hgt.customText=http://'+location.hostname+'/LDlinkRestWeb/tmp/track' + ldInputs.reference + '.txt'
-    //console.log(r2url)
-    $('#ldassoc-genome').prop('href',r2url);
-    
-    //console.dir(ldproxyInputs);
-    $('#ldassoc-results-link').attr('href','/LDlinkRestWeb/tmp/assoc' + ldInputs.reference + '.txt');
-    //console.log( $('#ldassoc-genome'))
-    //console.log(ldInputs);
-    var url = restServerUrl + "/ldassoc";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        data : ldInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        //JSON.parse() cleans up this json string.
-
-        // create bokeh object with output_backend=canvas from svg
-        var dataString = data[0];
-        var dataCanvas = new Object([dataString, data[1]]);
-
-        var jsonObjCanvas;
-        if(typeof dataCanvas == 'string') {
-            jsonObjCanvas = JSON.parse(dataCanvas);
-        } else {
-            jsonObjCanvas = dataCanvas;
-        }
-
-        // display graph if no errors
-        if (displayError(id, jsonObjCanvas) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            
-            $('#ldassoc-bokeh-graph').empty().append(dataCanvas);
- 
-            // place Download PDF button
-	        $('#' + id + '-export-dropdown').empty().prepend('<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldassoc-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="ldassoc-menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldassoc-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>');
-            $("#ldassoc-downloadSVG").click(function(e) {
-                e.preventDefault();
-                var assoc_plot = "/LDlinkRestWeb/tmp/assoc_plot_" + ldInputs.reference + ".svg";
-                window.open( assoc_plot, "_blank" )
-            });
-            $("#ldassoc-downloadPDF").click(function(e) {
-                e.preventDefault();
-                var assoc_plot = "/LDlinkRestWeb/tmp/assoc_plot_" + ldInputs.reference + ".pdf";
-                window.open( assoc_plot, "_blank" )
-            });
-            $("#ldassoc-downloadPNG").click(function(e) {
-                e.preventDefault();
-                var assoc_plot = "/LDlinkRestWeb/tmp/assoc_plot_" + ldInputs.reference + ".png";
-                window.open( assoc_plot, "_blank" )
-            });
-            $("#ldassoc-downloadJPEG").click(function(e) {
-                e.preventDefault();
-                var assoc_plot = "/LDlinkRestWeb/tmp/assoc_plot_" + ldInputs.reference + ".jpeg";
-                window.open( assoc_plot, "_blank" )
-            });
-
-            // enable button once .svg file is generated from subprocess
-            var fileURL = "/LDlinkRestWeb/tmp/assoc_plot_" + ldInputs.reference + ".jpeg";
-            checkFile(id, fileURL, 180);
-
-            $('#' + id + '-results-container').show();
-            getLDAssocResults('assoc'+ldInputs.reference+".json");
-        } else {
-            displayError(id, dataCanvas);
-        }
-        $("#"+id+"-loading").hide();
-
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-        setTimeout(function() {
-            var checkbox = $(".bk-toolbar-inspector").children().first();
-            $(checkbox).attr('id', 'hover');
-            $(checkbox).append('<label for="hover" class="sr-only">Hover Tool</label>');
-        }, 100);
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
-
+	var id = 'ldassoc';
+
+	var $btn = $('#' + id).button('loading');
+	var population = getPopulationCodes(id + '-population-codes');
+	var ldInputs = {
+		pop: population.join('+'),
+		filename: $('#ldassoc-file-label').val(),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		columns: new Object(),
+		calculateRegion: $('#assoc-region > button').val(),
+		gene: new Object(),
+		region: new Object(),
+		variant: new Object(),
+		genome_build: genomeBuild,
+		dprime: $('#assoc-matrix-color-r2').hasClass('active') ? 'False' : 'True',
+		transcript: $('#assoc-transcript').hasClass('active') ? 'False' : 'True',
+		//annotate: $("#assoc-annotate").hasClass('active') ? "True" :"False",
+		//annotate: $("#assoc-annotate").val(),
+		annotate: document.querySelector('input[name="ldassoc_options"]:checked')
+			.value,
+		useEx: $('#example-gwas').is(':checked') ? 'True' : 'False',
+	};
+
+	ldInputs.columns.chromosome = $('#assoc-chromosome > button').val();
+	ldInputs.columns.position = $('#assoc-position > button').val();
+	ldInputs.columns.pvalue = $('#assoc-p-value > button').val();
+	//gene
+	ldInputs.gene.name = $('#region-gene-name').val();
+	ldInputs.gene.basepair = $('#region-gene-base-pair-window').val();
+	ldInputs.gene.index = $('#region-gene-index').val();
+	//region
+	ldInputs.region.start = $('#region-region-start-coord').val();
+	ldInputs.region.end = $('#region-region-end-coord').val();
+	ldInputs.region.index = $('#region-region-index').val();
+	//variant
+	ldInputs.variant.index = $('#region-variant-index').val();
+	ldInputs.variant.basepair = $('#region-variant-base-pair-window').val();
+
+	var tempbuild = genomeBuild == 'grch37' ? 'hg19' : 'hg38';
+	var r2url =
+		'https://genome.ucsc.edu/cgi-bin/hgTracks?db=' +
+		tempbuild +
+		'&hgt.customText=http://' +
+		location.hostname +
+		'/LDlinkRestWeb/tmp/track' +
+		ldInputs.reference +
+		'.txt';
+	//console.log(r2url)
+	$('#ldassoc-genome').prop('href', r2url);
+
+	//console.dir(ldproxyInputs);
+	$('#ldassoc-results-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/assoc' + ldInputs.reference + '.txt'
+	);
+	//console.log( $('#ldassoc-genome'))
+	//console.log(ldInputs);
+	var url = restServerUrl + '/ldassoc';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		//JSON.parse() cleans up this json string.
+
+		// create bokeh object with output_backend=canvas from svg
+		var dataString = data[0];
+		var dataCanvas = new Object([dataString, data[1]]);
+
+		var jsonObjCanvas;
+		if (typeof dataCanvas == 'string') {
+			jsonObjCanvas = JSON.parse(dataCanvas);
+		} else {
+			jsonObjCanvas = dataCanvas;
+		}
+
+		// display graph if no errors
+		if (displayError(id, jsonObjCanvas) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+
+			$('#ldassoc-bokeh-graph').empty().append(dataCanvas);
+
+			// place Download PDF button
+			$('#' + id + '-export-dropdown')
+				.empty()
+				.prepend(
+					'<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldassoc-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="ldassoc-menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldassoc-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldassoc-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>'
+				);
+			$('#ldassoc-downloadSVG').click(function (e) {
+				e.preventDefault();
+				var assoc_plot =
+					'/LDlinkRestWeb/tmp/assoc_plot_' + ldInputs.reference + '.svg';
+				window.open(assoc_plot, '_blank');
+			});
+			$('#ldassoc-downloadPDF').click(function (e) {
+				e.preventDefault();
+				var assoc_plot =
+					'/LDlinkRestWeb/tmp/assoc_plot_' + ldInputs.reference + '.pdf';
+				window.open(assoc_plot, '_blank');
+			});
+			$('#ldassoc-downloadPNG').click(function (e) {
+				e.preventDefault();
+				var assoc_plot =
+					'/LDlinkRestWeb/tmp/assoc_plot_' + ldInputs.reference + '.png';
+				window.open(assoc_plot, '_blank');
+			});
+			$('#ldassoc-downloadJPEG').click(function (e) {
+				e.preventDefault();
+				var assoc_plot =
+					'/LDlinkRestWeb/tmp/assoc_plot_' + ldInputs.reference + '.jpeg';
+				window.open(assoc_plot, '_blank');
+			});
+
+			// enable button once .svg file is generated from subprocess
+			var fileURL =
+				'/LDlinkRestWeb/tmp/assoc_plot_' + ldInputs.reference + '.jpeg';
+			checkFile(id, fileURL, 180);
+
+			$('#' + id + '-results-container').show();
+			getLDAssocResults('assoc' + ldInputs.reference + '.json');
+		} else {
+			displayError(id, dataCanvas);
+		}
+		$('#' + id + '-loading').hide();
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+		setTimeout(function () {
+			var checkbox = $('.bk-toolbar-inspector').children().first();
+			$(checkbox).attr('id', 'hover');
+			$(checkbox).append(
+				'<label for="hover" class="sr-only">Hover Tool</label>'
+			);
+		}, 100);
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function updateLDhap() {
-
-    var id = "ldhap";
-
-    var $btn = $('#' + id).button('loading');
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var population = getPopulationCodes(id+'-population-codes');
-    var ldInputs = {
-        snps : snps,
-        pop : population.join("+"),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild
-    };
-    var url = restServerUrl + "/ldhap";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        data : ldInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        //JSON.parse() cleans up this json string.
-        var jsonObj;
-        if(typeof data == 'string') {
-            jsonObj = JSON.parse(data);
-        } else {
-            jsonObj = data;
-        }
-
-        if (displayError(id, jsonObj) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            $('#' + id + '-results-container').show();
-            $('#' + id + '-links-container').show();
-            var ldhapTable = formatLDhapData($.parseJSON(data));
-            $('#ldhap-haplotypes-column').attr('colspan',ldhapTable.footer.length);
-            ko.mapping.fromJS(ldhapTable, ldhapModel);
-            addLDHapHyperLinks(ldInputs.reference, ldhapTable);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldhap';
+
+	var $btn = $('#' + id).button('loading');
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var population = getPopulationCodes(id + '-population-codes');
+	var ldInputs = {
+		snps: snps,
+		pop: population.join('+'),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+	};
+	var url = restServerUrl + '/ldhap';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		//JSON.parse() cleans up this json string.
+		var jsonObj;
+		if (typeof data == 'string') {
+			jsonObj = JSON.parse(data);
+		} else {
+			jsonObj = data;
+		}
+
+		if (displayError(id, jsonObj) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+			$('#' + id + '-results-container').show();
+			$('#' + id + '-links-container').show();
+			var ldhapTable = formatLDhapData($.parseJSON(data));
+			$('#ldhap-haplotypes-column').attr('colspan', ldhapTable.footer.length);
+			ko.mapping.fromJS(ldhapTable, ldhapModel);
+			addLDHapHyperLinks(ldInputs.reference, ldhapTable);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function explodeLegalArray(entities) {
-    //Turn an arry into a legal statement to use in a scentense
-    //Example: array("Maryland", "New York", "Virginia")
-    // = "Maryland, New York, and Virgina"
-
-    var delimiter = ",";
-    var output;
-    if(entities.length == 0) {
-        return entities[0];
-    }
-
-    $.each(entities, function (key, value) {
-        if(key == 0) {
-            output = value;
-        } else if(key == entities.length-1) {
-            output += " & "+value;
-        } else {
-            output += delimiter+" "+value;
-        }
-    });
-    return output;
+	//Turn an arry into a legal statement to use in a scentense
+	//Example: array("Maryland", "New York", "Virginia")
+	// = "Maryland, New York, and Virgina"
+
+	var delimiter = ',';
+	var output;
+	if (entities.length == 0) {
+		return entities[0];
+	}
+
+	$.each(entities, function (key, value) {
+		if (key == 0) {
+			output = value;
+		} else if (key == entities.length - 1) {
+			output += ' & ' + value;
+		} else {
+			output += delimiter + ' ' + value;
+		}
+	});
+	return output;
 }
 
 function updateLDexpress() {
-    var id = "ldexpress";
-
-    var $btn = $('#' + id).button('loading');
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var population = getPopulationCodes(id + '-population-codes');
-    var tissues = $('#'+ id + '-tissue-codes').val();
-    // console.log("tissues", tissues);
-    var r2_d;
-    var window = $("#" + id + "-bp-window").val().replace(/\,/g, '');
-
-    if($('#ldexpress_ld_r2').hasClass('active')) {
-        r2_d = 'r2'; // i.e. R2
-    } else {
-        r2_d = 'd';  // i.e. Dprime
-    }
-
-    // var estimateWindowSizeMultiplier = window / 500000.0;
-    // var estimateSeconds = Math.round((snps.split("\n").length * 5 * estimateWindowSizeMultiplier));
-    // // console.log("estimate seconds", estimateSeconds);
-    // var estimateMinutes = estimateSeconds / 60;
-    // if (estimateSeconds < 60) {
-    //     $('#ldexpress-estimate-loading').text(estimateSeconds + " seconds");
-    // } else {
-    //     $('#ldexpress-estimate-loading').text(estimateMinutes.toFixed(2) + " minute(s)");
-    // }
-
-    var ldInputs = {
-        snps: snps,
-        pop: population.join("+"),
-        tissues: tissues.join("+"),
-        r2_d: r2_d,
-        r2_d_threshold: Number($("#" + id + "_r2_d_threshold").val()),
-        p_threshold: Number($("#" + id + "_p_threshold").val()),
-        window: window,
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild
-    };
-
-    //Show inital message
-    $('#new-ldexpress_wrapper').hide();
-    $('#new-ldexpress-query-warnings_wrapper').hide();
-    $('#ldexpress-initial-message').show();
-
-    //Update href on
-    //Set file links
-    $("#ldexpress-variants-annotated-link").attr('href', '/LDlinkRestWeb/tmp/express_variants_annotated' + ldInputs.reference + '.txt');
-    $("#ldexpress-variants-annotated-link").attr('target', 'express_variants_annotated' + ldInputs.reference);
-    // $("#ldexpress-details-link").attr('href', '/LDlinkRestWeb/tmp/details'+ldInputs.reference+'.txt');
-    // $("#ldexpress-details-link").attr('target', 'snp_details_'+ldInputs.reference);
-
-    // Set populations on LDThinned
-    //$('.ldexpress-populations').empty().append(explodeLegalArray(population));
-
-    var url = restServerUrl + "/ldexpress";
-    var ajaxRequest = $.ajax({
-        type : 'POST',
-        url : url,
-        data : JSON.stringify(ldInputs),
-        contentType : 'application/json' // JSON
-    });
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        var jsonObj=data;
-        // console.log(data);
-        if (displayError(id, jsonObj) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            $('#' + id + '-results-container').show();
-            $('#' + id + '-links-container').show();
-            $('#'+id+"-loading").hide();
-            initExpress(data, r2_d);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldexpress';
+
+	var $btn = $('#' + id).button('loading');
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var population = getPopulationCodes(id + '-population-codes');
+	var tissues = $('#' + id + '-tissue-codes').val();
+	// console.log("tissues", tissues);
+	var r2_d;
+	var window = $('#' + id + '-bp-window')
+		.val()
+		.replace(/\,/g, '');
+
+	if ($('#ldexpress_ld_r2').hasClass('active')) {
+		r2_d = 'r2'; // i.e. R2
+	} else {
+		r2_d = 'd'; // i.e. Dprime
+	}
+
+	// var estimateWindowSizeMultiplier = window / 500000.0;
+	// var estimateSeconds = Math.round((snps.split("\n").length * 5 * estimateWindowSizeMultiplier));
+	// // console.log("estimate seconds", estimateSeconds);
+	// var estimateMinutes = estimateSeconds / 60;
+	// if (estimateSeconds < 60) {
+	//     $('#ldexpress-estimate-loading').text(estimateSeconds + " seconds");
+	// } else {
+	//     $('#ldexpress-estimate-loading').text(estimateMinutes.toFixed(2) + " minute(s)");
+	// }
+
+	var ldInputs = {
+		snps: snps,
+		pop: population.join('+'),
+		tissues: tissues.join('+'),
+		r2_d: r2_d,
+		r2_d_threshold: Number($('#' + id + '_r2_d_threshold').val()),
+		p_threshold: Number($('#' + id + '_p_threshold').val()),
+		window: window,
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+	};
+
+	//Show inital message
+	$('#new-ldexpress_wrapper').hide();
+	$('#new-ldexpress-query-warnings_wrapper').hide();
+	$('#ldexpress-initial-message').show();
+
+	//Update href on
+	//Set file links
+	$('#ldexpress-variants-annotated-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/express_variants_annotated' +
+			ldInputs.reference +
+			'.txt'
+	);
+	$('#ldexpress-variants-annotated-link').attr(
+		'target',
+		'express_variants_annotated' + ldInputs.reference
+	);
+	// $("#ldexpress-details-link").attr('href', '/LDlinkRestWeb/tmp/details'+ldInputs.reference+'.txt');
+	// $("#ldexpress-details-link").attr('target', 'snp_details_'+ldInputs.reference);
+
+	// Set populations on LDThinned
+	//$('.ldexpress-populations').empty().append(explodeLegalArray(population));
+
+	var url = restServerUrl + '/ldexpress';
+	var ajaxRequest = $.ajax({
+		type: 'POST',
+		url: url,
+		data: JSON.stringify(ldInputs),
+		contentType: 'application/json', // JSON
+	});
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		var jsonObj = data;
+		// console.log(data);
+		if (displayError(id, jsonObj) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+			$('#' + id + '-results-container').show();
+			$('#' + id + '-links-container').show();
+			$('#' + id + '-loading').hide();
+			initExpress(data, r2_d);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function updateLDtrait() {
-    var id = "ldtrait";
-
-    var $btn = $('#' + id).button('loading');
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var population = getPopulationCodes(id+'-population-codes');
-    var r2_d;
-    var window = $("#" + id + "-bp-window").val().replace(/\,/g, '');
-    var ifContinue = document.getElementById("ldtrait-continue").value
-    
-    if($('#ldtrait_ld_r2').hasClass('active')) {
-        r2_d = 'r2'; // i.e. R2
-    } else {
-        r2_d = 'd';  // i.e. Dprime
-    }
-
-    var estimateWindowSizeMultiplier = window / 500000.0;
-    var estimateSeconds = Math.round((snps.split("\n").length * 5 * estimateWindowSizeMultiplier));
-    // console.log("estimate seconds", estimateSeconds);
-    var estimateMinutes = estimateSeconds / 60;
-    if (estimateSeconds < 60) {
-        $('#ldtrait-estimate-loading').text(estimateSeconds + " seconds");
-    } else {
-        $('#ldtrait-estimate-loading').text(estimateMinutes.toFixed(2) + " minute(s)");
-    }
-
-    var ldInputs = {
-        snps : snps,
-        pop : population.join("+"),
-        r2_d: r2_d,
-        r2_d_threshold: $("#"+id+"_r2_d_threshold").val(),
-        window: window,
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild,
-        ifContinue : ifContinue
-    };
-
-    //Show inital message
-    $('#new-ldtrait_wrapper').hide();
-    $('#new-ldtrait-query-warnings_wrapper').hide();
-    $('#ldtrait-initial-message').show();
-    $('#ldtrait-continue').attr("style","display:none")
-    $('#ldtrait-cancel').attr("style","display:none")
-    //Update href on
-    //Set file links
-    $("#ldtrait-variants-annotated-link").attr('href', '/LDlinkRestWeb/tmp/trait_variants_annotated' + ldInputs.reference + '.txt');
-    $("#ldtrait-variants-annotated-link").attr('target', 'trait_variants_annotated' + ldInputs.reference);
-    // $("#ldtrait-details-link").attr('href', '/LDlinkRestWeb/tmp/details'+ldInputs.reference+'.txt');
-    // $("#ldtrait-details-link").attr('target', 'snp_details_'+ldInputs.reference);
-
-    // Set populations on LDThinned
-    //$('.ldtrait-populations').empty().append(explodeLegalArray(population));
-
-    var url = restServerUrl + "/ldtrait";
-    var ajaxRequest = $.ajax({
-        type : 'POST',
-        url : url,
-        data : JSON.stringify(ldInputs),
-        contentType : 'application/json' // JSON
-    });
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        var jsonObj=data;
-        if (displayError(id, jsonObj) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            $('#' + id + '-results-container').show();
-            $('#' + id + '-links-container').show();
-            $('#'+id+"-loading").hide();
-            initTrait(data, r2_d);
-        }
-        if(data.warning != null){
-            if(data.warning.includes("timeout")){
-                $('#' + id + '-results-container').hide();
-                $('#' + id + '-links-container').hide();
-                $('#'+id+"-loading").hide();
-                $('#ldtrait-continue').attr("style","display:block")
-                $('#ldtrait-cancel').attr("style","display:block")
-            }
-        }
-        
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
-    document.getElementById("ldtrait-continue").value = "Continue";
+	var id = 'ldtrait';
+
+	var $btn = $('#' + id).button('loading');
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var population = getPopulationCodes(id + '-population-codes');
+	var r2_d;
+	var window = $('#' + id + '-bp-window')
+		.val()
+		.replace(/\,/g, '');
+	var ifContinue = document.getElementById('ldtrait-continue').value;
+
+	if ($('#ldtrait_ld_r2').hasClass('active')) {
+		r2_d = 'r2'; // i.e. R2
+	} else {
+		r2_d = 'd'; // i.e. Dprime
+	}
+
+	var estimateWindowSizeMultiplier = window / 500000.0;
+	var estimateSeconds = Math.round(
+		snps.split('\n').length * 5 * estimateWindowSizeMultiplier
+	);
+	// console.log("estimate seconds", estimateSeconds);
+	var estimateMinutes = estimateSeconds / 60;
+	if (estimateSeconds < 60) {
+		$('#ldtrait-estimate-loading').text(estimateSeconds + ' seconds');
+	} else {
+		$('#ldtrait-estimate-loading').text(
+			estimateMinutes.toFixed(2) + ' minute(s)'
+		);
+	}
+
+	var ldInputs = {
+		snps: snps,
+		pop: population.join('+'),
+		r2_d: r2_d,
+		r2_d_threshold: $('#' + id + '_r2_d_threshold').val(),
+		window: window,
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+		ifContinue: ifContinue,
+	};
+
+	//Show inital message
+	$('#new-ldtrait_wrapper').hide();
+	$('#new-ldtrait-query-warnings_wrapper').hide();
+	$('#ldtrait-initial-message').show();
+	$('#ldtrait-continue').attr('style', 'display:none');
+	$('#ldtrait-cancel').attr('style', 'display:none');
+	//Update href on
+	//Set file links
+	$('#ldtrait-variants-annotated-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/trait_variants_annotated' + ldInputs.reference + '.txt'
+	);
+	$('#ldtrait-variants-annotated-link').attr(
+		'target',
+		'trait_variants_annotated' + ldInputs.reference
+	);
+	// $("#ldtrait-details-link").attr('href', '/LDlinkRestWeb/tmp/details'+ldInputs.reference+'.txt');
+	// $("#ldtrait-details-link").attr('target', 'snp_details_'+ldInputs.reference);
+
+	// Set populations on LDThinned
+	//$('.ldtrait-populations').empty().append(explodeLegalArray(population));
+
+	var url = restServerUrl + '/ldtrait';
+	var ajaxRequest = $.ajax({
+		type: 'POST',
+		url: url,
+		data: JSON.stringify(ldInputs),
+		contentType: 'application/json', // JSON
+	});
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		var jsonObj = data;
+		if (displayError(id, jsonObj) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+			$('#' + id + '-results-container').show();
+			$('#' + id + '-links-container').show();
+			$('#' + id + '-loading').hide();
+			initTrait(data, r2_d);
+		}
+		if (data.warning != null) {
+			if (data.warning.includes('timeout')) {
+				$('#' + id + '-results-container').hide();
+				$('#' + id + '-links-container').hide();
+				$('#' + id + '-loading').hide();
+				$('#ldtrait-continue').attr('style', 'display:block');
+				$('#ldtrait-cancel').attr('style', 'display:block');
+			}
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
+	document.getElementById('ldtrait-continue').value = 'Continue';
 }
 
 function ldtraitContinue() {
-  document.getElementById("ldtrait-continue").value = "False";
-  //console.log("after click continue:"+document.getElementById("ldtrait-continue").value)
-  updateLDtrait()
-  $('#ldtrait-results-container').hide();
-  $('#ldtrait-links-container').hide();
-  $('#ldtrait-loading').hide();
-  $('#ldtrait-continue').attr("style","display:none")
-  $('#ldtrait-cancel').attr("style","display:none")
-  $('#ldtrait-message-warning').hide();
-  $('#ldtrait-loading').show();
+	document.getElementById('ldtrait-continue').value = 'False';
+	//console.log("after click continue:"+document.getElementById("ldtrait-continue").value)
+	updateLDtrait();
+	$('#ldtrait-results-container').hide();
+	$('#ldtrait-links-container').hide();
+	$('#ldtrait-loading').hide();
+	$('#ldtrait-continue').attr('style', 'display:none');
+	$('#ldtrait-cancel').attr('style', 'display:none');
+	$('#ldtrait-message-warning').hide();
+	$('#ldtrait-loading').show();
 }
 
 function ldtraitCancel() {
-  document.getElementById("ldtrait-continue").value = "Continue";
-  $('#ldtrait-results-container').hide();
-  $('#ldtrait-links-container').hide();
-  $('#ldtrait-loading').hide();
-  $('#ldtrait-continue').attr("style","display:none")
-  $('#ldtrait-cancel').attr("style","display:none")
-  $('#ldtrait-message-warning').hide();
+	document.getElementById('ldtrait-continue').value = 'Continue';
+	$('#ldtrait-results-container').hide();
+	$('#ldtrait-links-container').hide();
+	$('#ldtrait-loading').hide();
+	$('#ldtrait-continue').attr('style', 'display:none');
+	$('#ldtrait-cancel').attr('style', 'display:none');
+	$('#ldtrait-message-warning').hide();
 }
 
 function updateSNPclip() {
-    var id = "snpclip";
-
-    var $btn = $('#' + id).button('loading');
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var population = getPopulationCodes(id+'-population-codes');
-
-    var ldInputs = {
-        snps : snps,
-        pop : population.join("+"),
-        r2_threshold: $("#"+id+"_r2_threshold").val(),
-        maf_threshold: $("#"+id+"_maf_threshold").val(),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild
-    };
-
-    //Show inital message
-    $('#snpclip-details').hide();
-    $('#snpclip-warnings').hide();
-    $('#snpclip-initial-message').show();
-
-    //Update href on
-    //Set file links
-    $("#snpclip-snps-link").attr('href', '/LDlinkRestWeb/tmp/snp_list'+ldInputs.reference+'.txt');
-    $("#snpclip-snps-link").attr('target', 'snp_thin_list_'+ldInputs.reference);
-    $("#snpclip-details-link").attr('href', '/LDlinkRestWeb/tmp/details'+ldInputs.reference+'.txt');
-    $("#snpclip-details-link").attr('target', 'snp_details_'+ldInputs.reference);
-
-    // Set populations on LDThinned
-    //$('.snpclip-populations').empty().append(explodeLegalArray(population));
-
-    var url = restServerUrl + "/snpclip";
-    var ajaxRequest = $.ajax({
-        type : 'POST',
-        url : url,
-        data : JSON.stringify(ldInputs),
-        contentType : 'application/json' // JSON
-    });
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        var jsonObj=data;
-        if (displayError(id, jsonObj) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            $('#' + id + '-results-container').show();
-            $('#' + id + '-links-container').show();
-            $('#'+id+"-loading").hide();
-            initClip(data);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'snpclip';
+
+	var $btn = $('#' + id).button('loading');
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var population = getPopulationCodes(id + '-population-codes');
+
+	var ldInputs = {
+		snps: snps,
+		pop: population.join('+'),
+		r2_threshold: $('#' + id + '_r2_threshold').val(),
+		maf_threshold: $('#' + id + '_maf_threshold').val(),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+	};
+
+	//Show inital message
+	$('#snpclip-details').hide();
+	$('#snpclip-warnings').hide();
+	$('#snpclip-initial-message').show();
+
+	//Update href on
+	//Set file links
+	$('#snpclip-snps-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/snp_list' + ldInputs.reference + '.txt'
+	);
+	$('#snpclip-snps-link').attr('target', 'snp_thin_list_' + ldInputs.reference);
+	$('#snpclip-details-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/details' + ldInputs.reference + '.txt'
+	);
+	$('#snpclip-details-link').attr(
+		'target',
+		'snp_details_' + ldInputs.reference
+	);
+
+	// Set populations on LDThinned
+	//$('.snpclip-populations').empty().append(explodeLegalArray(population));
+
+	var url = restServerUrl + '/snpclip';
+	var ajaxRequest = $.ajax({
+		type: 'POST',
+		url: url,
+		data: JSON.stringify(ldInputs),
+		contentType: 'application/json', // JSON
+	});
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		var jsonObj = data;
+		if (displayError(id, jsonObj) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+			$('#' + id + '-results-container').show();
+			$('#' + id + '-links-container').show();
+			$('#' + id + '-loading').hide();
+			initClip(data);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function updateSNPchip() {
-    var id = "snpchip";
-
-    var $btn = $('#' + id).button('loading');
-    $("#collapseThree").removeClass("in");
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var platforms = [];
-
-    $('.affymetrix:checked').each(function() {
-        platforms.push($(this).val());
-    });
-    $('.illumina:checked').each(function() {
-        platforms.push($(this).val());
-    });
-
-
-    var ldInputs = {
-        snps : snps,
-        platforms: platforms.join("+"),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild
-    };
-    $('#snp_chip_list').attr('href', "/LDlinkRestWeb/tmp/details"+ldInputs.reference+".txt");
-    $('#snp_chip_list').attr('target', "chip_details"+ldInputs.reference+".txt");
-    //console.dir(ldInputs);
-    var url = restServerUrl + "/snpchip";
-    var ajaxRequest = $.ajax({
-        type : 'POST',
-        url : url,
-    data : JSON.stringify(ldInputs),
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        //data is returned as a string representation of JSON instead of JSON obj
-        var jsonObj=data;
-        if (displayError(id, jsonObj) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-            $('#' + id + '-results-container').show();
-            $('#' + id + '-links-container').show();
-            $('#'+id+"-loading").hide();
-            loadSNPChip(data);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'snpchip';
+
+	var $btn = $('#' + id).button('loading');
+	$('#collapseThree').removeClass('in');
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var platforms = [];
+
+	$('.affymetrix:checked').each(function () {
+		platforms.push($(this).val());
+	});
+	$('.illumina:checked').each(function () {
+		platforms.push($(this).val());
+	});
+
+	var ldInputs = {
+		snps: snps,
+		platforms: platforms.join('+'),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+	};
+	$('#snp_chip_list').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/details' + ldInputs.reference + '.txt'
+	);
+	$('#snp_chip_list').attr(
+		'target',
+		'chip_details' + ldInputs.reference + '.txt'
+	);
+	//console.dir(ldInputs);
+	var url = restServerUrl + '/snpchip';
+	var ajaxRequest = $.ajax({
+		type: 'POST',
+		url: url,
+		data: JSON.stringify(ldInputs),
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		//data is returned as a string representation of JSON instead of JSON obj
+		var jsonObj = data;
+		if (displayError(id, jsonObj) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+			$('#' + id + '-results-container').show();
+			$('#' + id + '-links-container').show();
+			$('#' + id + '-loading').hide();
+			loadSNPChip(data);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function initChip() {
-    //Setup the platform
-    var id = "snpchip";
-
-    var url = restServerUrl + "/snpchip_platforms";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        if (displayError(id, data) == false) {
-            //buildPopulationDropdownSNPchip(data);
-            buildPlatformSNPchip(data);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-
+	//Setup the platform
+	var id = 'snpchip';
+
+	var url = restServerUrl + '/snpchip_platforms';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		if (displayError(id, data) == false) {
+			//buildPopulationDropdownSNPchip(data);
+			buildPlatformSNPchip(data);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
 }
 
 function loadSNPChip(data) {
-    //Setup data and display
-    //snpchipData = [];
-    // = "This is about error";
-
-    //delete snpchipData["warning"];
-    //delete snpchipData["error"];
-
-    var snpchip = JSON.parse(data);
-
-    var all_platforms_used = [];
-    var newchip = [];
-    var snpData;
-    var obj;
-    var test = "";
-    var associated_platforms;
-    var total_platform_count = 0;
-
-    $.each(snpchip, function(row, detail) {
-        if(row.search("warning")>=0 ||row.search("error")>=0) {
-            //Print the warning somewhere on the screen.
-            if(row.search("warning")>=0) {
-                snpchipData["warning"] = detail;
-            }
-            if(row.search("error")>=0) {
-                snpchipData["error"] = detail;
-            }
-            //Remove this item
-            delete snpchip[row];
-        } else {
-            //Gather all platforms
-            //if(parseInt(row)< 1) {
-                associated_platforms = detail[2].split(",");
-                //console.log("associated_platforms: "+parseInt(row)+" "+detail[0]);
-                //console.dir(associated_platforms.sort());
-
-                $.each(detail[2].split(","), function(key, value){
-                    if(value != "") {
-                        all_platforms_used.push(value);
-                        test += key+") "+detail[2]+"\n";
-                    }
-                });
-            //}
-        }
-    });
-    //console.warn("All Platforms");
-    //console.log("Count: "+all_platforms_used.length);
-    //Find the unique one from all of the platforms
-    var used_platforms
-    var platform_list = all_platforms_used.unique();
-    var map = [];
-    var reversed_platform_list = [];
-    snpchipData["headers"] = [];
-    platform_list.sort();
-    /*
+	//Setup data and display
+	//snpchipData = [];
+	// = "This is about error";
+
+	//delete snpchipData["warning"];
+	//delete snpchipData["error"];
+
+	var snpchip = JSON.parse(data);
+
+	var all_platforms_used = [];
+	var newchip = [];
+	var snpData;
+	var obj;
+	var test = '';
+	var associated_platforms;
+	var total_platform_count = 0;
+
+	$.each(snpchip, function (row, detail) {
+		if (row.search('warning') >= 0 || row.search('error') >= 0) {
+			//Print the warning somewhere on the screen.
+			if (row.search('warning') >= 0) {
+				snpchipData['warning'] = detail;
+			}
+			if (row.search('error') >= 0) {
+				snpchipData['error'] = detail;
+			}
+			//Remove this item
+			delete snpchip[row];
+		} else {
+			//Gather all platforms
+			//if(parseInt(row)< 1) {
+			associated_platforms = detail[2].split(',');
+			//console.log("associated_platforms: "+parseInt(row)+" "+detail[0]);
+			//console.dir(associated_platforms.sort());
+
+			$.each(detail[2].split(','), function (key, value) {
+				if (value != '') {
+					all_platforms_used.push(value);
+					test += key + ') ' + detail[2] + '\n';
+				}
+			});
+			//}
+		}
+	});
+	//console.warn("All Platforms");
+	//console.log("Count: "+all_platforms_used.length);
+	//Find the unique one from all of the platforms
+	var used_platforms;
+	var platform_list = all_platforms_used.unique();
+	var map = [];
+	var reversed_platform_list = [];
+	snpchipData['headers'] = [];
+	platform_list.sort();
+	/*
     console.warn("Filtered list of  Platforms");
     console.log("Count: "+platform_list.length);
     console.log(test);
     */
-    //Now that we have the platform list... Map each platform.
-    $.each(snpchip, function(row, detail){
-        //Walk throught the platform_list and determine if it has the list... create a map for the table.
-        map = [];
-        used_platforms = detail[2].split(",");
-        //console.log("used_platforms:");
-        //console.dir(used_platforms);
-        //console.warn("row: "+row);
-        var platform_count = 0;
-
-        $.each(platform_list, function(key, value) {
-            //console.log(key+":"+value);
-            //console.info($.inArray(value, used_platforms));
-            if($.inArray(value, used_platforms) >= 0) {
-                map.push("&#x2713;");
-                platform_count++;
-                total_platform_count++;
-            } else {
-                map.push("&nbsp;");
-            }
-        });
-        //Split detail[1] into two parts
-        var chromo_position = detail[1].split(":");
-        obj = {
-            "rs_number" : anchorRSnumber(detail[0]),
-            "chromosome" : chromo_position[0],
-            "position" : anchorRSposition("chr"+detail[1], detail[0]),
-            "map" : map,
-            "rs_number_original" : detail[0],
-            "platform_count" : platform_count
-        };
-        //console.dir(obj);
-        newchip.push(obj);
-    });
-
-    $.each(platform_list, function(key, value) {
-        //reversed_platform_list.push(snpchipReverseLookup[value]);
-        obj ={
-            code: snpchipReverseLookup[value] !== undefined ?  snpchipReverseLookup[value] : snpchipReverseLookup[value.replace(/\sArray$/, "")],
-            platform: value
-        };
-        if(typeof obj.code === "undefined") {
-            /*
+	//Now that we have the platform list... Map each platform.
+	$.each(snpchip, function (row, detail) {
+		//Walk throught the platform_list and determine if it has the list... create a map for the table.
+		map = [];
+		used_platforms = detail[2].split(',');
+		//console.log("used_platforms:");
+		//console.dir(used_platforms);
+		//console.warn("row: "+row);
+		var platform_count = 0;
+
+		$.each(platform_list, function (key, value) {
+			//console.log(key+":"+value);
+			//console.info($.inArray(value, used_platforms));
+			if ($.inArray(value, used_platforms) >= 0) {
+				map.push('&#x2713;');
+				platform_count++;
+				total_platform_count++;
+			} else {
+				map.push('&nbsp;');
+			}
+		});
+		//Split detail[1] into two parts
+		var chromo_position = detail[1].split(':');
+		obj = {
+			rs_number: anchorRSnumber(detail[0]),
+			chromosome: chromo_position[0],
+			position: anchorRSposition('chr' + detail[1], detail[0]),
+			map: map,
+			rs_number_original: detail[0],
+			platform_count: platform_count,
+		};
+		//console.dir(obj);
+		newchip.push(obj);
+	});
+
+	$.each(platform_list, function (key, value) {
+		//reversed_platform_list.push(snpchipReverseLookup[value]);
+		obj = {
+			code:
+				snpchipReverseLookup[value] !== undefined
+					? snpchipReverseLookup[value]
+					: snpchipReverseLookup[value.replace(/\sArray$/, '')],
+			platform: value,
+		};
+		if (typeof obj.code === 'undefined') {
+			/*
             console.info("Reverse lookup does appear to exist");
             console.info("Removing key "+key+" from platform_list below.");
             console.info("This value doesn't seem to have a code: "+value);
             console.log("platform_list:");
             console.dir(platform_list);
             */
-            obj ={
-                code: "unknown code",
-                platform: value
-            };
-            snpchipData["headers"].push(obj);
-        } else {
-            snpchipData["headers"].push(obj);
-        }
-    });
-    snpchipData["snpchip"] = newchip;
-    var header_len = snpchipData["headers"].length;
-    if( header_len < 20) {
-        //calcualte width
-        $('#snpchip-table-right').attr('width', 100+(header_len*30));
-    } else {
-        $('#snpchip-table-right').removeAttr('width');
-    }
-
-    ko.mapping.fromJS(snpchipData, snpchipModel);
-
-    $('#snpchip-message-warning-content').empty();
-    checkAlert("snpchip", snpchipData.warning, "warning", true);
-    checkAlert("snpchip", snpchipData.error, "error", false);
-    //Display warning if an rs has no platform arrays
-    if(total_platform_count == 0) {
-        //Hide table and display an error.
-        $('#snpchip-results-container').hide();
-
-    }
+			obj = {
+				code: 'unknown code',
+				platform: value,
+			};
+			snpchipData['headers'].push(obj);
+		} else {
+			snpchipData['headers'].push(obj);
+		}
+	});
+	snpchipData['snpchip'] = newchip;
+	var header_len = snpchipData['headers'].length;
+	if (header_len < 20) {
+		//calcualte width
+		$('#snpchip-table-right').attr('width', 100 + header_len * 30);
+	} else {
+		$('#snpchip-table-right').removeAttr('width');
+	}
+
+	ko.mapping.fromJS(snpchipData, snpchipModel);
+
+	$('#snpchip-message-warning-content').empty();
+	checkAlert('snpchip', snpchipData.warning, 'warning', true);
+	checkAlert('snpchip', snpchipData.error, 'error', false);
+	//Display warning if an rs has no platform arrays
+	if (total_platform_count == 0) {
+		//Hide table and display an error.
+		$('#snpchip-results-container').hide();
+	}
 }
 
 function checkAlert(elementId, message, type, displayResults) {
-    //type is either 'warning' or 'error'
-    var prefix;
-    if(type == 'warning') {
-        prefix = elementId+'-message-warning';
-    } else {
-        prefix = elementId+'-message';
-    }
-    $('#'+prefix).hide();
-    if (typeof message !== 'undefined' && message.length > 0) {
-        $('#'+prefix+'-content').html("<div>"+message.replace(/(?:\r\n|\r|\n)/g, '<br />')+"</div>");
-        $('#'+prefix).show();
-        if (typeof displayResults !== 'undefined' && displayResults) {
-            $('#'+elementId+'-results-container').show();
-        } else {
-            $('#'+elementId+'-results-container').hide();
-        }
-    }
+	//type is either 'warning' or 'error'
+	var prefix;
+	if (type == 'warning') {
+		prefix = elementId + '-message-warning';
+	} else {
+		prefix = elementId + '-message';
+	}
+	$('#' + prefix).hide();
+	if (typeof message !== 'undefined' && message.length > 0) {
+		$('#' + prefix + '-content').html(
+			'<div>' + message.replace(/(?:\r\n|\r|\n)/g, '<br />') + '</div>'
+		);
+		$('#' + prefix).show();
+		if (typeof displayResults !== 'undefined' && displayResults) {
+			$('#' + elementId + '-results-container').show();
+		} else {
+			$('#' + elementId + '-results-container').hide();
+		}
+	}
 }
 
 function populateSNPlistLDexpress(data) {
-    //clear out the list
-    $("#ldexpress-snp-list").empty();
-    //Add the clipped list
-    $.each(data, function( index, value ){
-        $("#ldexpress-snp-list").append(
-            $("<tr>", { class: 'ldexpress-snps-list-rows', id: 'snp__row__' + value }).append(
-                $("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
-                    $('<input />', { type: 'checkbox', id: 'filter__snp__' + value, value: 'snp__' + value, 'style': "margin-right: 4px;", class: 'ldexpress-data-filters', 'title': 'Filter on variant' }),
-                    $('<label />', { 'for': 'filter__snp__' + value, text: value, 'style': 'white-space: nowrap;', 'title': value })
-                ])
-            )
-        )
-    });
+	//clear out the list
+	$('#ldexpress-snp-list').empty();
+	//Add the clipped list
+	$.each(data, function (index, value) {
+		$('#ldexpress-snp-list').append(
+			$('<tr>', {
+				class: 'ldexpress-snps-list-rows',
+				id: 'snp__row__' + value,
+			}).append(
+				$('<td>', { style: 'white-space: nowrap; width: 150px;' }).append([
+					$('<input />', {
+						type: 'checkbox',
+						id: 'filter__snp__' + value,
+						value: 'snp__' + value,
+						style: 'margin-right: 4px;',
+						class: 'ldexpress-data-filters',
+						title: 'Filter on variant',
+					}),
+					$('<label />', {
+						for: 'filter__snp__' + value,
+						text: value,
+						style: 'white-space: nowrap;',
+						title: value,
+					}),
+				])
+			)
+		);
+	});
 }
 
 function populateGeneslistLDexpress(data) {
-    //clear out the list
-    $("#ldexpress-genes-list").empty();
-    //Add the clipped list
-    $.each(data, function( index, value ){
-        $("#ldexpress-genes-list").append(
-            $("<tr>", { class: 'ldexpress-genes-list-rows', id: 'gene__row__' + value.split("__")[0] }).append(
-                $("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
-                    $('<input />', { type: 'checkbox', id: 'filter__gene__' + value.split("__")[0], value: 'gene__' + value.split("__")[0], 'style': "margin-right: 4px;", class: 'ldexpress-data-filters', 'title': 'Filter on gene' }),
-                    $('<label />', { 'for': 'filter__gene__' + value.split("__")[0], text: value.split("__")[0], 'style': 'white-space: nowrap;', 'title': value.split("__")[0] })
-                ])
-            )
-        )
-    });
+	//clear out the list
+	$('#ldexpress-genes-list').empty();
+	//Add the clipped list
+	$.each(data, function (index, value) {
+		$('#ldexpress-genes-list').append(
+			$('<tr>', {
+				class: 'ldexpress-genes-list-rows',
+				id: 'gene__row__' + value.split('__')[0],
+			}).append(
+				$('<td>', { style: 'white-space: nowrap; width: 150px;' }).append([
+					$('<input />', {
+						type: 'checkbox',
+						id: 'filter__gene__' + value.split('__')[0],
+						value: 'gene__' + value.split('__')[0],
+						style: 'margin-right: 4px;',
+						class: 'ldexpress-data-filters',
+						title: 'Filter on gene',
+					}),
+					$('<label />', {
+						for: 'filter__gene__' + value.split('__')[0],
+						text: value.split('__')[0],
+						style: 'white-space: nowrap;',
+						title: value.split('__')[0],
+					}),
+				])
+			)
+		);
+	});
 }
 
 function populateTissueslistLDexpress(data) {
-    //clear out the list
-    $("#ldexpress-tissues-list").empty();
-    //Add the clipped list
-    $.each(data, function( index, value ){
-        $("#ldexpress-tissues-list").append(
-            $("<tr>", { class: 'ldexpress-tissues-list-rows', id: 'tissue__row__' + value.split("__")[1] }).append(
-                $("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
-                    $('<input />', { type: 'checkbox', id: 'filter__tissue__' + value.split("__")[1], value: 'tissue__' + value.split("__")[1], 'style': 'margin-right: 4px;', class: 'ldexpress-data-filters', 'title': 'Filter on tissue' }),
-                    $('<label />', { 'for': 'filter__tissue__' +  value.split("__")[1], text: value.split("__")[0], 'style': 'white-space: nowrap;', 'title': value.split("__")[0] })
-                ])
-            )
-        )
-    });
+	//clear out the list
+	$('#ldexpress-tissues-list').empty();
+	//Add the clipped list
+	$.each(data, function (index, value) {
+		$('#ldexpress-tissues-list').append(
+			$('<tr>', {
+				class: 'ldexpress-tissues-list-rows',
+				id: 'tissue__row__' + value.split('__')[1],
+			}).append(
+				$('<td>', { style: 'white-space: nowrap; width: 150px;' }).append([
+					$('<input />', {
+						type: 'checkbox',
+						id: 'filter__tissue__' + value.split('__')[1],
+						value: 'tissue__' + value.split('__')[1],
+						style: 'margin-right: 4px;',
+						class: 'ldexpress-data-filters',
+						title: 'Filter on tissue',
+					}),
+					$('<label />', {
+						for: 'filter__tissue__' + value.split('__')[1],
+						text: value.split('__')[0],
+						style: 'white-space: nowrap;',
+						title: value.split('__')[0],
+					}),
+				])
+			)
+		);
+	});
 }
 
 function populateSNPlistLDtrait(data) {
-    //clear out the list
-    $("#ldtrait-snp-list").empty();
-    //Add the clipped list
-    $.each(data.thinned_snps, function( index, value ){
-        $("#ldtrait-snp-list").append(
-            $("<tr>").append(
-                $("<td>").append(
-                    $("<a>")
-                        .attr('id', value)
-                        .attr('title', 'View details.')
-                        .append(value)
-                    )
-                )
-            )
-    });
-
+	//clear out the list
+	$('#ldtrait-snp-list').empty();
+	//Add the clipped list
+	$.each(data.thinned_snps, function (index, value) {
+		$('#ldtrait-snp-list').append(
+			$('<tr>').append(
+				$('<td>').append(
+					$('<a>')
+						.attr('id', value)
+						.attr('title', 'View details.')
+						.append(value)
+				)
+			)
+		);
+	});
 }
 
 function populateSNPlist(data) {
-
-    //clear out the list
-    $("#snpclip-snp-list").empty();
-    //Add the clipped list
-    $.each(data.snp_list, function( index, value ){
-        $("#snpclip-snp-list").append(
-            $("<tr>").append(
-                $("<td>").append(
-                    $("<a>")
-                        .attr('id', value)
-                        .attr('title', 'View details.')
-                        .append(value)
-                    )
-                )
-            )
-    });
-
+	//clear out the list
+	$('#snpclip-snp-list').empty();
+	//Add the clipped list
+	$.each(data.snp_list, function (index, value) {
+		$('#snpclip-snp-list').append(
+			$('<tr>').append(
+				$('<td>').append(
+					$('<a>')
+						.attr('id', value)
+						.attr('title', 'View details.')
+						.append(value)
+				)
+			)
+		);
+	});
 }
 
 function anchorRSnumber(rs_number) {
-    //var server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
-    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
-    var raw_rs_number = rs_number.substring(2);
-    var params = {
-        rs : raw_rs_number
-    };
-    //var url = server + "?" + $.param(params);
-    var url = server + rs_number;
-    return '<a href="'+url+'" target="rs_number_'+rs_number+'">'+rs_number+'</a>';
+	//var server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+	var server = 'http://www.ncbi.nlm.nih.gov/snp/';
+	var raw_rs_number = rs_number.substring(2);
+	var params = {
+		rs: raw_rs_number,
+	};
+	//var url = server + "?" + $.param(params);
+	var url = server + rs_number;
+	return (
+		'<a href="' +
+		url +
+		'" target="rs_number_' +
+		rs_number +
+		'">' +
+		rs_number +
+		'</a>'
+	);
 }
 
 function anchorRSposition(coord, rs_number) {
-    //
-    // Genome Browser:
-    //
-    //hide_chr = hide_chr || false;
-
-    if(coord.toUpperCase() == "NA")
-        return "NA";
-
-    server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
-    // snp1-coord
-    var positions = coord.split(":");
-    var chr = positions[0];
-    var mid_value = parseInt(positions[1]);
-    var offset = 250;
-    var range = (mid_value - offset) + "-" + (mid_value + offset);
-    var position = chr + ":" + range;
-    params = {
-        db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
-        position : position,
-        snp151 : 'pack',
-        'hgFind.matches' : rs_number
-    };
-    var url = server + "?" + $.param(params);
-    //if(hide_chr) {
-    //  return '<a href="'+url+'" target="coord_'+coord+'">'+positions[1]+'</a>';
-    //} else {
-    return '<a href="'+url+'" target="coord_'+coord+'">'+coord+'</a>';
-    //}
-}
-
-function populateSNPwarnings(data) {
-
-    snpclipData.warnings = [];
-
-    $.each(data.filtered, function( index, value ){
-
-        var filtered = {
-            rs_number: index,
-            position: value[0],
-            alleles: value[1],
-            comment: value[2],
-            rs_number_link: anchorRSnumber(index),
-            position_link: anchorRSposition(value[0], index)
-        };
-
-        if(filtered.comment != undefined) {
-            if(!filtered.comment.includes("Variant kept.") && !filtered.comment.includes("Variant in LD")) {
-                // Place message on the warning table.
-                // console.log("Push to warnings: " + filtered.rs_number + " " + filtered.comment);
-                snpclipData.warnings.push(filtered);
-
-                // Remove rs_numbers with warnings from thinned snp_list
-                var index = data.snp_list.indexOf(filtered.rs_number);
-                if (index > -1) {
-                    data.snp_list.splice(index, 1);
-                }   
-                
-            }
-        } else {
-            // console.log("filtered.comment is UNDEFINED " + filtered.rs_number);
-            // console.log(JSON.stringify(filtered));
-            snpclipData.warnings.push(filtered);
-
-            // Remove rs_numbers with warnings from thinned snp_list
-            var index = data.snp_list.indexOf(filtered.rs_number);
-            if (index > -1) {
-                data.snp_list.splice(index, 1);
-            }   
-            
-        }
-    });
-
-    //console.log("Warning Data");
-    //console.dir(snpclipData.warnings);
-
-    if(snpclipData.warnings.length == 0) {
-        $('#snpclip-warning').hide();
-    } else {
-        $('#snpclip-warning').show();
-    }
-    ko.mapping.fromJS(snpclipData, snpclipModel);
-
-    // Populate Thinned SNP List after rs_numbers that triggered warnings are removed
-    populateSNPlist(data);
+	//
+	// Genome Browser:
+	//
+	//hide_chr = hide_chr || false;
+
+	if (coord.toUpperCase() == 'NA') return 'NA';
+
+	server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
+	// snp1-coord
+	var positions = coord.split(':');
+	var chr = positions[0];
+	var mid_value = parseInt(positions[1]);
+	var offset = 250;
+	var range = mid_value - offset + '-' + (mid_value + offset);
+	var position = chr + ':' + range;
+	params = {
+		db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
+		position: position,
+		snp151: 'pack',
+		'hgFind.matches': rs_number,
+	};
+	var url = server + '?' + $.param(params);
+	//if(hide_chr) {
+	//  return '<a href="'+url+'" target="coord_'+coord+'">'+positions[1]+'</a>';
+	//} else {
+	return '<a href="' + url + '" target="coord_' + coord + '">' + coord + '</a>';
+	//}
+}
 
+function populateSNPwarnings(data) {
+	snpclipData.warnings = [];
+
+	$.each(data.filtered, function (index, value) {
+		var filtered = {
+			rs_number: index,
+			position: value[0],
+			alleles: value[1],
+			comment: value[2],
+			rs_number_link: anchorRSnumber(index),
+			position_link: anchorRSposition(value[0], index),
+		};
+
+		if (filtered.comment != undefined) {
+			if (
+				!filtered.comment.includes('Variant kept.') &&
+				!filtered.comment.includes('Variant in LD')
+			) {
+				// Place message on the warning table.
+				// console.log("Push to warnings: " + filtered.rs_number + " " + filtered.comment);
+				snpclipData.warnings.push(filtered);
+
+				// Remove rs_numbers with warnings from thinned snp_list
+				var index = data.snp_list.indexOf(filtered.rs_number);
+				if (index > -1) {
+					data.snp_list.splice(index, 1);
+				}
+			}
+		} else {
+			// console.log("filtered.comment is UNDEFINED " + filtered.rs_number);
+			// console.log(JSON.stringify(filtered));
+			snpclipData.warnings.push(filtered);
+
+			// Remove rs_numbers with warnings from thinned snp_list
+			var index = data.snp_list.indexOf(filtered.rs_number);
+			if (index > -1) {
+				data.snp_list.splice(index, 1);
+			}
+		}
+	});
+
+	//console.log("Warning Data");
+	//console.dir(snpclipData.warnings);
+
+	if (snpclipData.warnings.length == 0) {
+		$('#snpclip-warning').hide();
+	} else {
+		$('#snpclip-warning').show();
+	}
+	ko.mapping.fromJS(snpclipData, snpclipModel);
+
+	// Populate Thinned SNP List after rs_numbers that triggered warnings are removed
+	populateSNPlist(data);
 }
 
 function loadLDexpressDetails(data, sort) {
-    // console.log("ldExpressRaw", data);
-    // console.log("rs_number", rs_number);
+	// console.log("ldExpressRaw", data);
+	// console.log("rs_number", rs_number);
 
-    RefreshTableSort('#new-ldexpress', data.details["results"], sort, 3, 4);
-    // $('#new-ldexpress_wrapper').show();
-    // var oTable = $('#new-ldexpress').dataTable();
-    // // Hide the second column after initialisation
-    // oTable.fnSetColumnVis( 0, false );
-    // $('#ldexpress-detail-title').text("Details for " + rs_number);
+	RefreshTableSort('#new-ldexpress', data.details['results'], sort, 3, 4);
+	// $('#new-ldexpress_wrapper').show();
+	// var oTable = $('#new-ldexpress').dataTable();
+	// // Hide the second column after initialisation
+	// oTable.fnSetColumnVis( 0, false );
+	// $('#ldexpress-detail-title').text("Details for " + rs_number);
 }
 
 function loadLDexpressQueryWarnings(data) {
-    // console.log("ldExpressRaw", data);
+	// console.log("ldExpressRaw", data);
 
-    RefreshTable('#new-ldexpress-query-warnings', data.details.queryWarnings);
-    $('#new-ldexpress-query-warnings_wrapper').show();
+	RefreshTable('#new-ldexpress-query-warnings', data.details.queryWarnings);
+	$('#new-ldexpress-query-warnings_wrapper').show();
 }
 
 function loadLDtraitDetails(data, rs_number, sort) {
-    // console.log("ldTraitRaw", data);
-    // console.log("rs_number", rs_number);
+	// console.log("ldTraitRaw", data);
+	// console.log("rs_number", rs_number);
 
-    RefreshTableSort('#new-ldtrait', data.details[rs_number], sort, 4, 5);
-    $('#new-ldtrait_wrapper').show();
+	RefreshTableSort('#new-ldtrait', data.details[rs_number], sort, 4, 5);
+	$('#new-ldtrait_wrapper').show();
 
-    $('#ldtrait-detail-title').text("Details for " + rs_number);
+	$('#ldtrait-detail-title').text('Details for ' + rs_number);
 }
 
 function loadLDtraitQueryWarnings(data) {
-    // console.log("ldTraitRaw", data);
+	// console.log("ldTraitRaw", data);
 
-    RefreshTable('#new-ldtrait-query-warnings', data.details.queryWarnings);
-    $('#new-ldtrait-query-warnings_wrapper').show();
+	RefreshTable('#new-ldtrait-query-warnings', data.details.queryWarnings);
+	$('#new-ldtrait-query-warnings_wrapper').show();
 }
 
 function loadSNPdetails(data, rs_number) {
-
-    snpclipData.details =[];
-    /*
+	snpclipData.details = [];
+	/*
     console.log("Here is the rs_number to populate");
     console.log("rs_number: "+rs_number);
     console.dir(data.details);
@@ -3139,555 +4073,595 @@ function loadSNPdetails(data, rs_number) {
     console.log("Found one::::");
     console.dir(data.details[rs_number]);
     */
-    var found = false;
-    var match = 'Variant in LD with ' + rs_number;
-;
-
-    $.each(data.details, function( index, value ){
-        var detail = {
-            rs_number: index,
-            position: value[0],
-            alleles: value[1],
-            comment: value[2],
-            rs_number_link: anchorRSnumber(index),
-            position_link: anchorRSposition(value[0], index)
-        };
-        if(detail.rs_number == rs_number) {
-            found = true;
-        }
-        if(found) {
-            if(detail.comment != undefined) {
-                if((detail.rs_number == rs_number && detail.comment.includes("Variant kept.")) ||
-                    detail.comment.includes(match)) {
-                    snpclipData.details.push(detail);
-                } 
-            } 
-            // else {
-            //     console.log("detail.comment is UNDEFINED " + detail.rs_numbers);
-            //     // console.log(JSON.stringify(detail));
-            //     snpclipData.warnings.push(detail);
-            // }
-        }
-    });
-
-    //console.dir(snpclipData);
-    //console.log(JSON.stringify(snpclipData));
-    ko.mapping.fromJS(snpclipData, snpclipModel);
-    $('#snpclip-detail-title').text("Details for "+rs_number);
+	var found = false;
+	var match = 'Variant in LD with ' + rs_number;
+	$.each(data.details, function (index, value) {
+		var detail = {
+			rs_number: index,
+			position: value[0],
+			alleles: value[1],
+			comment: value[2],
+			rs_number_link: anchorRSnumber(index),
+			position_link: anchorRSposition(value[0], index),
+		};
+		if (detail.rs_number == rs_number) {
+			found = true;
+		}
+		if (found) {
+			if (detail.comment != undefined) {
+				if (
+					(detail.rs_number == rs_number &&
+						detail.comment.includes('Variant kept.')) ||
+					detail.comment.includes(match)
+				) {
+					snpclipData.details.push(detail);
+				}
+			}
+			// else {
+			//     console.log("detail.comment is UNDEFINED " + detail.rs_numbers);
+			//     // console.log(JSON.stringify(detail));
+			//     snpclipData.warnings.push(detail);
+			// }
+		}
+	});
+
+	//console.dir(snpclipData);
+	//console.log(JSON.stringify(snpclipData));
+	ko.mapping.fromJS(snpclipData, snpclipModel);
+	$('#snpclip-detail-title').text('Details for ' + rs_number);
 }
 
 function initExpress(data, r2_d) {
-
-    ldExpressRaw = data;
-    ldExpressSort = r2_d;
-
-    populateSNPlistLDexpress(data.thinned_snps);
-    populateGeneslistLDexpress(data.thinned_genes);
-    populateTissueslistLDexpress(data.thinned_tissues);
-
-    // advanced filter click action
-    $('input[type=checkbox].ldexpress-data-filters').on('click', function(e) {
-        $('#ldexpress-snp-list').show();
-        $('#ldexpress-initial-message').hide();
-        $('#new-ldexpress_wrapper').show();
-        $('#new-ldexpress-query-warnings_wrapper').hide();
-        $('#ldexpress-initial-message').hide();
-
-        var selected_snps = [];
-        var selected_genes = [];
-        var selected_tissues = [];
-
-        $('input[type=checkbox].ldexpress-data-filters').each(function() {
-            if ($(this).is(':checked')) {
-                var category = $(this).attr('value').split('__')[0];
-                var checked_val = $(this).attr('value').split('__')[1];
-                if (category === "snp") {
-                    selected_snps.push(checked_val);
-                }
-                if (category === "gene") {
-                    selected_genes.push(checked_val);
-                }
-                if (category === "tissue") {
-                    var displayTissueName = data.thinned_tissues.filter(function(el) {
-                        return el.split("__")[1] === checked_val;
-                    })
-                    selected_tissues.push(displayTissueName[0].split("__")[0].replace("(", "\\(").replace(")", "\\)"));
-                }
-            }
-         });
-
-        // console.log("selected_snps", selected_snps);
-        // console.log("selected_genes", selected_genes);
-        // console.log("selected_tissues", selected_tissues);
-        //  apply filters
-        var oTable = $('#new-ldexpress').dataTable();
-        oTable.fnFilter(selected_snps.join("|"), 0, true, false);
-        oTable.fnFilter(selected_genes.join("|"), 5, true, false);
-        oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
-        var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        var newSNPs = [];
-        var newGenes = [];
-        var newTissues = [];
-        newData.forEach(function(row) {
-            newSNPs.push(row[0]);
-            newGenes.push(row[5].split("__")[0]);
-            newTissues.push(row[7].split("__")[1]);
-        });
-        newSNPs = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        newGenes = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        newTissues = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        // console.log("newSNPs", newSNPs);
-        // console.log("newGenes", newGenes);
-        // console.log("newTissues", newTissues);
-        $('.ldexpress-snps-list-rows').each(function(i, obj) {
-            if (newSNPs.includes($(obj).attr('id').split('__')[2])) {
-                $(obj).show();
-            } else {
-                $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-                $(obj).hide();
-            }
-        });
-        $('.ldexpress-genes-list-rows').each(function(i, obj) {
-            if (newGenes.includes($(obj).attr('id').split('__')[2])) {
-                $(obj).show();
-            } else {
-                $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-                $(obj).hide();
-            }
-        });
-        $('.ldexpress-tissues-list-rows').each(function(i, obj) {
-            if (newTissues.includes($(obj).attr('id').split('__')[2])) {
-                $(obj).show();
-            } else {
-                $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-                $(obj).hide();
-            }
-        });
-
-
-        // // refresh all filter options when other snp filters added
-        // if (selected_snps.length > 0) {
-        //     oTable.fnFilter(selected_snps.join("|"), 0, true, false);
-        //     if ($(e.target).attr("id").split("__")[1] === "snp") {
-        //         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //         var newGenes = [];
-        //         var newTissues = [];
-        //         newData.forEach(function(row) {
-        //             newGenes.push(row[5].split("__")[0]);
-        //             newTissues.push(row[7].split("__")[0]);
-        //         });
-        //         var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         $('.ldexpress-genes-list-rows').each(function(i, obj) {
-        //             if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //             }
-        //         });
-        //         var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         $('.ldexpress-tissues-list-rows').each(function(i, obj) {
-        //             if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //             }
-        //         });
-        //     }
-        // } else {
-        //     oTable.fnFilter("", 0, true, false);
-        //     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //     var newGenes = [];
-        //     var newTissues = [];
-        //     newData.forEach(function(row) {
-        //         newGenes.push(row[5].split("__")[0]);
-        //         newTissues.push(row[7].split("__")[0]);
-        //     });
-        //     var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-genes-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        //     var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-tissues-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        // }
-        // // refresh all filter options when gene filters added
-        // if (selected_genes.length > 0) {
-        //     oTable.fnFilter(selected_genes.join("|"), 5, true, false);
-        //     // show only tissues available for gene
-        //     // only register on gene click
-        //     if ($(e.target).attr("id").split("__")[1] === "gene") {
-        //         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //         var newTissues = [];
-        //         var newSNPs = [];
-        //         newData.forEach(function(row) {
-        //             newTissues.push(row[7].split("__")[1]);
-        //             newSNPs.push(row[0]);
-        //         });
-        //         var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         $('.ldexpress-tissues-list-rows').each(function(i, obj) {
-        //             if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //             }
-        //         });
-        //         var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         console.log("newSNPsDistinct", newSNPsDistinct);
-        //         $('.ldexpress-snps-list-rows').each(function(i, obj) {
-        //             if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 console.log("reached 1");
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //                 console.log("reached 2");
-        //             }
-        //         });
-        //     }
-        // } else {
-        //     oTable.fnFilter("", 5, true, false);
-        //     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //     var newTissues = [];
-        //     var newSNPs = [];
-        //     newData.forEach(function(row) {
-        //         newTissues.push(row[7].split("__")[0]);
-        //         newSNPs.push(row[0]);
-        //     });
-        //     var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-tissues-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        //     var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-snps-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        // }
-        // // refresh all filter options when other tissue filters added
-        // if (selected_tissues.length > 0) {
-        //     oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
-        //     // show only genes available for tissue
-        //     // only register on tissue click
-        //     if ($(e.target).attr("id").split("__")[1] === "tissue") {
-        //         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //         var newGenes = [];
-        //         var newSNPs = [];
-        //         newData.forEach(function(row) {
-        //             newGenes.push(row[5].split("__")[0]);
-        //             newSNPs.push(row[0]);
-        //         });
-        //         var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         $('.ldexpress-genes-list-rows').each(function(i, obj) {
-        //             if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //             }
-        //         });
-        //         var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //         $('.ldexpress-snps-list-rows').each(function(i, obj) {
-        //             if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
-        //                 $(obj).show();
-        //             } else {
-        //                 $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
-        //                 $(obj).hide();
-        //             }
-        //         });
-        //     }
-        // } else {
-        //     oTable.fnFilter("", 7, true, false);
-        //     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
-        //     var newGenes = [];
-        //     var newSNPs = [];
-        //     newData.forEach(function(row) {
-        //         newGenes.push(row[5].split("__")[0]);
-        //         newSNPs.push(row[0]);
-        //     });
-        //     var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-genes-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        //     var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
-        //     $('.ldexpress-snps-list-rows').each(function(i, obj) {
-        //         $(obj).show();
-        //     });
-        // }
-    });
-
-    if(data.details.queryWarnings && data.details.queryWarnings.aaData.length > 0) {
-        $('#ldexpress-query-warnings-button').show();
-    } else {
-        $('#ldexpress-query-warnings-button').hide();
-    }
-    // init data table
-    $('#ldexpress-snp-list').show();
-    $('#ldexpress-initial-message').hide();
-    loadLDexpressDetails(ldExpressRaw, ldExpressSort);
-    $('#new-ldexpress_wrapper').show();
-    $('#new-ldexpress-query-warnings_wrapper').hide();
-    $('#ldexpress-initial-message').hide();
+	ldExpressRaw = data;
+	ldExpressSort = r2_d;
+
+	populateSNPlistLDexpress(data.thinned_snps);
+	populateGeneslistLDexpress(data.thinned_genes);
+	populateTissueslistLDexpress(data.thinned_tissues);
+
+	// advanced filter click action
+	$('input[type=checkbox].ldexpress-data-filters').on('click', function (e) {
+		$('#ldexpress-snp-list').show();
+		$('#ldexpress-initial-message').hide();
+		$('#new-ldexpress_wrapper').show();
+		$('#new-ldexpress-query-warnings_wrapper').hide();
+		$('#ldexpress-initial-message').hide();
+
+		var selected_snps = [];
+		var selected_genes = [];
+		var selected_tissues = [];
+
+		$('input[type=checkbox].ldexpress-data-filters').each(function () {
+			if ($(this).is(':checked')) {
+				var category = $(this).attr('value').split('__')[0];
+				var checked_val = $(this).attr('value').split('__')[1];
+				if (category === 'snp') {
+					selected_snps.push(checked_val);
+				}
+				if (category === 'gene') {
+					selected_genes.push(checked_val);
+				}
+				if (category === 'tissue') {
+					var displayTissueName = data.thinned_tissues.filter(function (el) {
+						return el.split('__')[1] === checked_val;
+					});
+					selected_tissues.push(
+						displayTissueName[0]
+							.split('__')[0]
+							.replace('(', '\\(')
+							.replace(')', '\\)')
+					);
+				}
+			}
+		});
+
+		// console.log("selected_snps", selected_snps);
+		// console.log("selected_genes", selected_genes);
+		// console.log("selected_tissues", selected_tissues);
+		//  apply filters
+		var oTable = $('#new-ldexpress').dataTable();
+		oTable.fnFilter(selected_snps.join('|'), 0, true, false);
+		oTable.fnFilter(selected_genes.join('|'), 5, true, false);
+		oTable.fnFilter(selected_tissues.join('|'), 7, true, false);
+		var newData = Array.from(oTable._('tr', { filter: 'applied' }));
+		var newSNPs = [];
+		var newGenes = [];
+		var newTissues = [];
+		newData.forEach(function (row) {
+			newSNPs.push(row[0]);
+			newGenes.push(row[5].split('__')[0]);
+			newTissues.push(row[7].split('__')[1]);
+		});
+		newSNPs = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		newGenes = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		newTissues = newTissues
+			.filter((item, i, ar) => ar.indexOf(item) === i)
+			.sort();
+		// console.log("newSNPs", newSNPs);
+		// console.log("newGenes", newGenes);
+		// console.log("newTissues", newTissues);
+		$('.ldexpress-snps-list-rows').each(function (i, obj) {
+			if (newSNPs.includes($(obj).attr('id').split('__')[2])) {
+				$(obj).show();
+			} else {
+				$('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop(
+					'checked',
+					false
+				);
+				$(obj).hide();
+			}
+		});
+		$('.ldexpress-genes-list-rows').each(function (i, obj) {
+			if (newGenes.includes($(obj).attr('id').split('__')[2])) {
+				$(obj).show();
+			} else {
+				$('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop(
+					'checked',
+					false
+				);
+				$(obj).hide();
+			}
+		});
+		$('.ldexpress-tissues-list-rows').each(function (i, obj) {
+			if (newTissues.includes($(obj).attr('id').split('__')[2])) {
+				$(obj).show();
+			} else {
+				$('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop(
+					'checked',
+					false
+				);
+				$(obj).hide();
+			}
+		});
+
+		// // refresh all filter options when other snp filters added
+		// if (selected_snps.length > 0) {
+		//     oTable.fnFilter(selected_snps.join("|"), 0, true, false);
+		//     if ($(e.target).attr("id").split("__")[1] === "snp") {
+		//         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//         var newGenes = [];
+		//         var newTissues = [];
+		//         newData.forEach(function(row) {
+		//             newGenes.push(row[5].split("__")[0]);
+		//             newTissues.push(row[7].split("__")[0]);
+		//         });
+		//         var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         $('.ldexpress-genes-list-rows').each(function(i, obj) {
+		//             if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//             }
+		//         });
+		//         var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         $('.ldexpress-tissues-list-rows').each(function(i, obj) {
+		//             if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//             }
+		//         });
+		//     }
+		// } else {
+		//     oTable.fnFilter("", 0, true, false);
+		//     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//     var newGenes = [];
+		//     var newTissues = [];
+		//     newData.forEach(function(row) {
+		//         newGenes.push(row[5].split("__")[0]);
+		//         newTissues.push(row[7].split("__")[0]);
+		//     });
+		//     var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-genes-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		//     var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-tissues-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		// }
+		// // refresh all filter options when gene filters added
+		// if (selected_genes.length > 0) {
+		//     oTable.fnFilter(selected_genes.join("|"), 5, true, false);
+		//     // show only tissues available for gene
+		//     // only register on gene click
+		//     if ($(e.target).attr("id").split("__")[1] === "gene") {
+		//         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//         var newTissues = [];
+		//         var newSNPs = [];
+		//         newData.forEach(function(row) {
+		//             newTissues.push(row[7].split("__")[1]);
+		//             newSNPs.push(row[0]);
+		//         });
+		//         var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         $('.ldexpress-tissues-list-rows').each(function(i, obj) {
+		//             if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//             }
+		//         });
+		//         var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         console.log("newSNPsDistinct", newSNPsDistinct);
+		//         $('.ldexpress-snps-list-rows').each(function(i, obj) {
+		//             if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 console.log("reached 1");
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//                 console.log("reached 2");
+		//             }
+		//         });
+		//     }
+		// } else {
+		//     oTable.fnFilter("", 5, true, false);
+		//     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//     var newTissues = [];
+		//     var newSNPs = [];
+		//     newData.forEach(function(row) {
+		//         newTissues.push(row[7].split("__")[0]);
+		//         newSNPs.push(row[0]);
+		//     });
+		//     var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-tissues-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		//     var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-snps-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		// }
+		// // refresh all filter options when other tissue filters added
+		// if (selected_tissues.length > 0) {
+		//     oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
+		//     // show only genes available for tissue
+		//     // only register on tissue click
+		//     if ($(e.target).attr("id").split("__")[1] === "tissue") {
+		//         var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//         var newGenes = [];
+		//         var newSNPs = [];
+		//         newData.forEach(function(row) {
+		//             newGenes.push(row[5].split("__")[0]);
+		//             newSNPs.push(row[0]);
+		//         });
+		//         var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         $('.ldexpress-genes-list-rows').each(function(i, obj) {
+		//             if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//             }
+		//         });
+		//         var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//         $('.ldexpress-snps-list-rows').each(function(i, obj) {
+		//             if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
+		//                 $(obj).show();
+		//             } else {
+		//                 $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
+		//                 $(obj).hide();
+		//             }
+		//         });
+		//     }
+		// } else {
+		//     oTable.fnFilter("", 7, true, false);
+		//     var newData = Array.from(oTable._('tr', {"filter":"applied"}));
+		//     var newGenes = [];
+		//     var newSNPs = [];
+		//     newData.forEach(function(row) {
+		//         newGenes.push(row[5].split("__")[0]);
+		//         newSNPs.push(row[0]);
+		//     });
+		//     var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-genes-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		//     var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
+		//     $('.ldexpress-snps-list-rows').each(function(i, obj) {
+		//         $(obj).show();
+		//     });
+		// }
+	});
+
+	if (
+		data.details.queryWarnings &&
+		data.details.queryWarnings.aaData.length > 0
+	) {
+		$('#ldexpress-query-warnings-button').show();
+	} else {
+		$('#ldexpress-query-warnings-button').hide();
+	}
+	// init data table
+	$('#ldexpress-snp-list').show();
+	$('#ldexpress-initial-message').hide();
+	loadLDexpressDetails(ldExpressRaw, ldExpressSort);
+	$('#new-ldexpress_wrapper').show();
+	$('#new-ldexpress-query-warnings_wrapper').hide();
+	$('#ldexpress-initial-message').hide();
 }
 
 function initTrait(data, r2_d) {
+	ldTraitRaw = data;
+	ldTraitSort = r2_d;
 
-    ldTraitRaw = data;
-    ldTraitSort = r2_d;
-
-    populateSNPlistLDtrait(data);
+	populateSNPlistLDtrait(data);
 
-    if(data.details.queryWarnings && data.details.queryWarnings.aaData.length > 0) {
-        $('#ldtrait-query-warnings-button').show();
-    } else {
-        $('#ldtrait-query-warnings-button').hide();
-    }
+	if (
+		data.details.queryWarnings &&
+		data.details.queryWarnings.aaData.length > 0
+	) {
+		$('#ldtrait-query-warnings-button').show();
+	} else {
+		$('#ldtrait-query-warnings-button').hide();
+	}
 }
 
 function initExpressTissues() {
-    var id = "ldexpress";
-    var url = restServerUrl + "/ldexpress_tissues";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        contentType : 'application/json' // JSON
-    });
-    ajaxRequest.success(function(data) {
-        if (displayError(id, data) == false) {
-            buildTissueDropdown(id + "-tissue-codes", data);
-        } else {
-            buildTissueDropdown("ldexpress-tissue-codes", data);
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        var errorObj = {
-            "error": "Failed to retrieve tissues from database."
-        }
-        displayError(id, errorObj)
-        buildTissueDropdown("ldexpress-tissue-codes", "{}");
-        // displayCommFail(id, jqXHR, textstatus);
-    });
+	var id = 'ldexpress';
+	var url = restServerUrl + '/ldexpress_tissues';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		contentType: 'application/json', // JSON
+	});
+	ajaxRequest.success(function (data) {
+		if (displayError(id, data) == false) {
+			buildTissueDropdown(id + '-tissue-codes', data);
+		} else {
+			buildTissueDropdown('ldexpress-tissue-codes', data);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		var errorObj = {
+			error: 'Failed to retrieve tissues from database.',
+		};
+		displayError(id, errorObj);
+		buildTissueDropdown('ldexpress-tissue-codes', '{}');
+		// displayCommFail(id, jqXHR, textstatus);
+	});
 }
 
 function initTraitTimestamp() {
-    var id = "ldtrait";
-    var url = restServerUrl + "/ldtrait_timestamp";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        contentType : 'application/json' // JSON
-    });
-    ajaxRequest.success(function(data) {
-        if (displayError(id, data) == false) {
-            var datetime = new Date(JSON.parse(data).$date);
-            var date = datetime.toLocaleDateString("en-US");
-            var time = datetime.toLocaleTimeString("en-US", {hour: '2-digit', minute:'2-digit'});
-            var timezone =  datetime.toString().match(/([A-Z]+[\+-][0-9]+)/)[1];
-            $('#ldtrait-timestamp').text(date + ", " + time + " (" + timezone + ")");
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
+	var id = 'ldtrait';
+	var url = restServerUrl + '/ldtrait_timestamp';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		contentType: 'application/json', // JSON
+	});
+	ajaxRequest.success(function (data) {
+		if (displayError(id, data) == false) {
+			var datetime = new Date(JSON.parse(data).$date);
+			var date = datetime.toLocaleDateString('en-US');
+			var time = datetime.toLocaleTimeString('en-US', {
+				hour: '2-digit',
+				minute: '2-digit',
+			});
+			var timezone = datetime.toString().match(/([A-Z]+[\+-][0-9]+)/)[1];
+			$('#ldtrait-timestamp').text(date + ', ' + time + ' (' + timezone + ')');
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
 }
 
 function initClip(data) {
+	ldClipRaw = data;
 
-    ldClipRaw = data;
-
-    populateSNPwarnings(data);
-    // populateSNPlist(data);
-    //loadSNPdetails(data, rs_number);
-    if(snpclipData.warnings.length == 0) {
-        $('#snpclip-warnings-button').hide();
-    } else {
-        $('#snpclip-warnings-button').show();
-    }
+	populateSNPwarnings(data);
+	// populateSNPlist(data);
+	//loadSNPdetails(data, rs_number);
+	if (snpclipData.warnings.length == 0) {
+		$('#snpclip-warnings-button').hide();
+	} else {
+		$('#snpclip-warnings-button').show();
+	}
 }
 
 function formatLDhapData(data) {
-
-    //console.log("get the two main parts of the data as hplotypes and snps");
-    //var indels = [];
-    var haplotypes = data.haplotypes;
-
-    //console.dir(haplotypes);
-
-    var snps = data.snps;
-    var ldhapTable = {
-        footer : [],
-        rows : []
-    };
-    //Get the indels from the haplotypes
-    $.each( haplotypes, function( key, value ) {
-        haplotypes[key].indels = value.Haplotype.split("_");
-    });
-
-    // Convert haplotypes to footer
-    for (key in haplotypes) {
-        //console.log(key);
-        //console.dir(haplotypes[key]);
-        var obj = {
-            Count : haplotypes[key].Count,
-            Frequency : haplotypes[key].Frequency,
-            Haplotype : haplotypes[key].indels
-            /* Haplotype : ["A", "GGA", "-", 'G'] */
-        };
-        // Add Haplotypes with a frequency of 1% or greater.
-        if (haplotypes[key].Frequency * 100 > 1) {
-            ldhapTable.footer.push(obj);
-        }
-    }
-    // Convert snps to rows.
-    for (key in snps) {
-        var obj = {
-            Alleles : snps[key].Alleles,
-            Coord : snps[key].Coord,
-            RS : snps[key].RS,
-            Haplotypes : []
-        };
-        ldhapTable.rows.push(obj);
-    }
-    // Add haplotypesHTML
-    $.each(ldhapTable.rows, function(index, value) {
-        // Get all the haplotypes in pivot order
-        $.each(ldhapTable.footer, function(index2, value2) {
-
-            value.Haplotypes[index2] = value2.Haplotype[index];
-
-        });
-    });
-
-    //console.log('ldhapTable');
-    //console.dir(ldhapTable);
-    var obj = {
-        out_final : ldhapTable
-    }
-    //console.dir(obj);
-    //console.info("LDhap ENDS here:");
-
-    return ldhapTable;
+	//console.log("get the two main parts of the data as hplotypes and snps");
+	//var indels = [];
+	var haplotypes = data.haplotypes;
+
+	//console.dir(haplotypes);
+
+	var snps = data.snps;
+	var ldhapTable = {
+		footer: [],
+		rows: [],
+	};
+	//Get the indels from the haplotypes
+	$.each(haplotypes, function (key, value) {
+		haplotypes[key].indels = value.Haplotype.split('_');
+	});
+
+	// Convert haplotypes to footer
+	for (key in haplotypes) {
+		//console.log(key);
+		//console.dir(haplotypes[key]);
+		var obj = {
+			Count: haplotypes[key].Count,
+			Frequency: haplotypes[key].Frequency,
+			Haplotype: haplotypes[key].indels,
+			/* Haplotype : ["A", "GGA", "-", 'G'] */
+		};
+		// Add Haplotypes with a frequency of 1% or greater.
+		if (haplotypes[key].Frequency * 100 > 1) {
+			ldhapTable.footer.push(obj);
+		}
+	}
+	// Convert snps to rows.
+	for (key in snps) {
+		var obj = {
+			Alleles: snps[key].Alleles,
+			Coord: snps[key].Coord,
+			RS: snps[key].RS,
+			Haplotypes: [],
+		};
+		ldhapTable.rows.push(obj);
+	}
+	// Add haplotypesHTML
+	$.each(ldhapTable.rows, function (index, value) {
+		// Get all the haplotypes in pivot order
+		$.each(ldhapTable.footer, function (index2, value2) {
+			value.Haplotypes[index2] = value2.Haplotype[index];
+		});
+	});
+
+	//console.log('ldhapTable');
+	//console.dir(ldhapTable);
+	var obj = {
+		out_final: ldhapTable,
+	};
+	//console.dir(obj);
+	//console.info("LDhap ENDS here:");
+
+	return ldhapTable;
 }
 
 function updateLDmatrix() {
-    var id = "ldmatrix";
-
-    var $btn = $('#' + id).button('loading');
-
-    var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
-    var population = getPopulationCodes(id+'-population-codes');
-    var r2_d;
-    $("#ldmatrix-legend-r2").attr('src', 'LDmatrix_legend.png');
-    //$("#ldmatrix-legend-r2").attr('src', 'LDmatrix_legend_R2.png');
-    //$("#ldmatrix-legend-d").attr('src', 'LDmatrix_legend_Dprime_Blue.png');
-
-    if($('#matrix_color_r2').hasClass('active')) {
-        r2_d='r2'; // i.e. R2
-        //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
-    } else {
-        r2_d='d';  // i.e.  Dprime
-        //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
-    }
-
-    var ldmatrixInputs = {
-        snps : snps,
-        pop : population.join("+"),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild,
-        r2_d : r2_d,
-        collapseTranscript: $("#matrix_collapse_transcripts").hasClass('active'),
-        annotate: document.querySelector('input[name="ldmatrix_options"]:checked').value
-    };
-    //console.log('ldmatrixInputs');
-    //console.dir(ldmatrixInputs);
-
-    var url = restServerUrl + "/ldmatrix";
-    var ajaxRequest = $.ajax({
-        type : 'GET',
-        url : url,
-        data : ldmatrixInputs
-    });
-
-    ajaxRequest.success(function(data) {
-        // if(typeof data == 'string') {
-        //     $('#ldmatrix-bokeh-graph').empty().append(data);
-        //     $('#' + id + '-progress-container').hide();
-        //     $('#' + id + '-results-container').show();
-        //     getLDmatrixResults(ldmatrixInputs.reference + ".json",
-        //             ldmatrixInputs.reference);
-        // } else {
-        //     displayError(id, data);
-        // }
-
-        // create bokeh object with output_backend=canvas from svg
-        var dataString = data;
-        var dataCanvas = new Object([dataString]);
-
-        var jsonObjCanvas;
-        if(typeof dataCanvas == 'string') {
-            jsonObjCanvas = JSON.parse(dataCanvas);
-        } else {
-            jsonObjCanvas = dataCanvas;
-        }
-
-        // generate shown canvas graph and hidden svg graph
-        if (displayError(id, jsonObjCanvas) == false) {
-            $('#ldmatrix-bokeh-graph').empty().append(dataCanvas);
-
-            // place Download PDF button
-	        $('#' + id + '-export-dropdown').empty().prepend('<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldmatrix-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldmatrix-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>');
-            $("#ldmatrix-downloadSVG").click(function(e) {
-                e.preventDefault();
-                var matrix_plot = "/LDlinkRestWeb/tmp/matrix_plot_" + ldmatrixInputs.reference + ".svg";
-                window.open( matrix_plot, "_blank" )
-            });
-            $("#ldmatrix-downloadPDF").click(function(e) {
-                e.preventDefault();
-                var matrix_plot = "/LDlinkRestWeb/tmp/matrix_plot_" + ldmatrixInputs.reference + ".pdf";
-                window.open( matrix_plot, "_blank" )
-            });
-            $("#ldmatrix-downloadPNG").click(function(e) {
-                e.preventDefault();
-                var matrix_plot = "/LDlinkRestWeb/tmp/matrix_plot_" + ldmatrixInputs.reference + ".png";
-                window.open( matrix_plot, "_blank" )
-            });
-            $("#ldmatrix-downloadJPEG").click(function(e) {
-                e.preventDefault();
-                var matrix_plot = "/LDlinkRestWeb/tmp/matrix_plot_" + ldmatrixInputs.reference + ".jpeg";
-                window.open( matrix_plot, "_blank" )
-            });
-            
-            // enable button once .svg file is generated from subprocess
-            var fileURL = "/LDlinkRestWeb/tmp/matrix_plot_" + ldmatrixInputs.reference + ".jpeg";
-            checkFile(id, fileURL, 180);
-
-            $('#' + id + '-results-container').show();
-            getLDmatrixResults(ldmatrixInputs.reference + ".json", ldmatrixInputs.reference);
-        } else {
-            displayError(id, dataCanvas);
-        }
-
-        $("#"+id+"-loading").hide();
-
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-        setTimeout(function(){var checkbox=$(".bk-toolbar-inspector").children().first();
-        $(checkbox).attr('id', 'hover');
-        $(checkbox).append('<label for="hover" class="sr-only">Hover Tool</label>');},100);
-    });
-
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldmatrix';
+
+	var $btn = $('#' + id).button('loading');
+
+	var snps = DOMPurify.sanitize($('#' + id + '-file-snp-numbers').val());
+	var population = getPopulationCodes(id + '-population-codes');
+	var r2_d;
+	$('#ldmatrix-legend-r2').attr('src', 'LDmatrix_legend.png');
+	//$("#ldmatrix-legend-r2").attr('src', 'LDmatrix_legend_R2.png');
+	//$("#ldmatrix-legend-d").attr('src', 'LDmatrix_legend_Dprime_Blue.png');
+
+	if ($('#matrix_color_r2').hasClass('active')) {
+		r2_d = 'r2'; // i.e. R2
+		//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
+	} else {
+		r2_d = 'd'; // i.e.  Dprime
+		//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
+	}
+
+	var ldmatrixInputs = {
+		snps: snps,
+		pop: population.join('+'),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+		r2_d: r2_d,
+		collapseTranscript: $('#matrix_collapse_transcripts').hasClass('active'),
+		annotate: document.querySelector('input[name="ldmatrix_options"]:checked')
+			.value,
+	};
+	//console.log('ldmatrixInputs');
+	//console.dir(ldmatrixInputs);
+
+	var url = restServerUrl + '/ldmatrix';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldmatrixInputs,
+	});
+
+	ajaxRequest.success(function (data) {
+		// if(typeof data == 'string') {
+		//     $('#ldmatrix-bokeh-graph').empty().append(data);
+		//     $('#' + id + '-progress-container').hide();
+		//     $('#' + id + '-results-container').show();
+		//     getLDmatrixResults(ldmatrixInputs.reference + ".json",
+		//             ldmatrixInputs.reference);
+		// } else {
+		//     displayError(id, data);
+		// }
+
+		// create bokeh object with output_backend=canvas from svg
+		var dataString = data;
+		var dataCanvas = new Object([dataString]);
+
+		var jsonObjCanvas;
+		if (typeof dataCanvas == 'string') {
+			jsonObjCanvas = JSON.parse(dataCanvas);
+		} else {
+			jsonObjCanvas = dataCanvas;
+		}
+
+		// generate shown canvas graph and hidden svg graph
+		if (displayError(id, jsonObjCanvas) == false) {
+			$('#ldmatrix-bokeh-graph').empty().append(dataCanvas);
+
+			// place Download PDF button
+			$('#' + id + '-export-dropdown')
+				.empty()
+				.prepend(
+					'<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldmatrix-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldmatrix-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldmatrix-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>'
+				);
+			$('#ldmatrix-downloadSVG').click(function (e) {
+				e.preventDefault();
+				var matrix_plot =
+					'/LDlinkRestWeb/tmp/matrix_plot_' + ldmatrixInputs.reference + '.svg';
+				window.open(matrix_plot, '_blank');
+			});
+			$('#ldmatrix-downloadPDF').click(function (e) {
+				e.preventDefault();
+				var matrix_plot =
+					'/LDlinkRestWeb/tmp/matrix_plot_' + ldmatrixInputs.reference + '.pdf';
+				window.open(matrix_plot, '_blank');
+			});
+			$('#ldmatrix-downloadPNG').click(function (e) {
+				e.preventDefault();
+				var matrix_plot =
+					'/LDlinkRestWeb/tmp/matrix_plot_' + ldmatrixInputs.reference + '.png';
+				window.open(matrix_plot, '_blank');
+			});
+			$('#ldmatrix-downloadJPEG').click(function (e) {
+				e.preventDefault();
+				var matrix_plot =
+					'/LDlinkRestWeb/tmp/matrix_plot_' +
+					ldmatrixInputs.reference +
+					'.jpeg';
+				window.open(matrix_plot, '_blank');
+			});
+
+			// enable button once .svg file is generated from subprocess
+			var fileURL =
+				'/LDlinkRestWeb/tmp/matrix_plot_' + ldmatrixInputs.reference + '.jpeg';
+			checkFile(id, fileURL, 180);
+
+			$('#' + id + '-results-container').show();
+			getLDmatrixResults(
+				ldmatrixInputs.reference + '.json',
+				ldmatrixInputs.reference
+			);
+		} else {
+			displayError(id, dataCanvas);
+		}
+
+		$('#' + id + '-loading').hide();
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+		setTimeout(function () {
+			var checkbox = $('.bk-toolbar-inspector').children().first();
+			$(checkbox).attr('id', 'hover');
+			$(checkbox).append(
+				'<label for="hover" class="sr-only">Hover Tool</label>'
+			);
+		}, 100);
+	});
+
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function addLDMatrixHyperLinks(request) {
-    $('#ldmatrix-DPrime').attr('href', '/LDlinkRestWeb/tmp/d_prime_' + request + '.txt');
-    $('#ldmatrix-R2').attr('href', '/LDlinkRestWeb/tmp/r2_' + request + '.txt');
+	$('#ldmatrix-DPrime').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/d_prime_' + request + '.txt'
+	);
+	$('#ldmatrix-R2').attr('href', '/LDlinkRestWeb/tmp/r2_' + request + '.txt');
 }
 /*
 function updateLDproxyProgressBar(id, seconds) {
@@ -3777,900 +4751,1026 @@ function createPopulationDropdown(id) {
 */
 
 function updateLDproxy() {
-    var id = "ldproxy";
-    var $btn = $('#' + id).button('loading');
-    var population = getPopulationCodes(id+'-population-codes');
-    var r2_d;
-    var windowSize = $("#" + id + "-bp-window").val().replace(/\,/g, '');
-
-    if($('#proxy_color_r2').hasClass('active')) {
-        r2_d='r2'; // i.e. R2
-        $('#ldproxy-genome').html("View R<sup>2</sup> data in UCSC Genome Browser");
-        //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
-    } else {
-        r2_d='d';  // i.e.  Dprime
-        $('#ldproxy-genome').html("View D' data in UCSC Genome Browser");
-        //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
-    }
-
-    var ldproxyInputs = {
-        "var" : $('#ldproxy-snp').val(),
-        pop : population.join("+"),
-        reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
-        genome_build: genomeBuild,
-        r2_d : r2_d,
-        window: windowSize,
-        collapseTranscript: $("#proxy_collapse_transcripts").hasClass('active'),
-        annotate: document.querySelector('input[name="ldproxy_options"]:checked').value
-    };
-
-    updateHistoryURL(id, ldproxyInputs);
-    //console.log(ldproxyInputs)
-    //console.log(location.hostname);
-
-    var proxy_build = genomeBuild == 'grch37' ? 'hg19' : 'hg38'
-    $('#ldproxy-genome').attr('href',
-        'https://genome.ucsc.edu/cgi-bin/hgTracks?db=' + proxy_build + '&hgt.customText=http://'+location.hostname+'/LDlinkRestWeb/tmp/track'
-        + ldproxyInputs.reference + '.txt');
-   
-    $('#ldproxy-results-link').attr('href','/LDlinkRestWeb/tmp/proxy' + ldproxyInputs.reference + '.txt');
-    var url = restServerUrl + "/ldproxy";
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url,
-        data : ldproxyInputs
-    });
-    ajaxRequest.success(function(data) {
-        // if (displayError(id, data) == false) {
-        //     $('#' + id + '-progress-container').hide();
-        //     $('#ldproxy-bokeh-graph').empty().append(data);
-        //     $('#' + id + '-results-container').show();
-        //     getLDProxyResults('proxy'+ldproxyInputs.reference+".json");
-        // }
-        // $("#"+id+"-loading").hide();
-
-        // create bokeh object with output_backend=canvas from svg
-        var dataString = data;
-        var dataCanvas = new Object([dataString]);
-
-        var jsonObjCanvas;
-        if(typeof dataCanvas == 'string') {
-            jsonObjCanvas = JSON.parse(dataCanvas);
-        } else {
-            jsonObjCanvas = dataCanvas;
-        }
-
-        // display graph if no errors
-        if (displayError(id, jsonObjCanvas) == false) {
-            switch(genomeBuild) {
-                case "grch37":
-                    $('.' + id + '-position-genome-build-header').text("GRCh37");
-                    break;
-                case "grch38":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38");
-                    break;
-                case "grch38_high_coverage":
-                    $('.' + id + '-position-genome-build-header').text("GRCh38 High Coverage");
-                    break;
-            }
-
-            $('#ldproxy-bokeh-graph').empty().append(dataCanvas);
- 
-            // place Download PDF button
-	        $('#' + id + '-export-dropdown').empty().prepend('<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldproxy-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldproxy-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>');
-            $("#ldproxy-downloadSVG").click(function(e) {
-                e.preventDefault();
-                var proxy_plot = "/LDlinkRestWeb/tmp/proxy_plot_" + ldproxyInputs.reference + ".svg";
-                window.open( proxy_plot, "_blank" )
-            });
-            $("#ldproxy-downloadPDF").click(function(e) {
-                e.preventDefault();
-                var proxy_plot = "/LDlinkRestWeb/tmp/proxy_plot_" + ldproxyInputs.reference + ".pdf";
-                window.open( proxy_plot, "_blank" )
-            });
-            $("#ldproxy-downloadPNG").click(function(e) {
-                e.preventDefault();
-                var proxy_plot = "/LDlinkRestWeb/tmp/proxy_plot_" + ldproxyInputs.reference + ".png";
-                window.open( proxy_plot, "_blank" )
-            });
-            $("#ldproxy-downloadJPEG").click(function(e) {
-                e.preventDefault();
-                var proxy_plot = "/LDlinkRestWeb/tmp/proxy_plot_" + ldproxyInputs.reference + ".jpeg";
-                window.open( proxy_plot, "_blank" )
-            });
-
-            // enable button once .svg file is generated from subprocess
-            var fileURL = "/LDlinkRestWeb/tmp/proxy_plot_" + ldproxyInputs.reference + ".jpeg";
-            checkFile(id, fileURL, 180);
-
-            $('#' + id + '-results-container').show();
-            getLDProxyResults('proxy'+ldproxyInputs.reference+".json");
-        } else {
-            displayError(id, dataCanvas);
-        }
-        $("#"+id+"-loading").hide();
-
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-        setTimeout(function(){var checkbox=$(".bk-toolbar-inspector").children().first();
-        $(checkbox).attr('id', 'hover');
-        $(checkbox).append('<label for="hover" class="sr-only">Hover Tool</label>');},100);
-    });
+	var id = 'ldproxy';
+	var $btn = $('#' + id).button('loading');
+	var population = getPopulationCodes(id + '-population-codes');
+	var r2_d;
+	var windowSize = $('#' + id + '-bp-window')
+		.val()
+		.replace(/\,/g, '');
+
+	if ($('#proxy_color_r2').hasClass('active')) {
+		r2_d = 'r2'; // i.e. R2
+		$('#ldproxy-genome').html('View R<sup>2</sup> data in UCSC Genome Browser');
+		//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
+	} else {
+		r2_d = 'd'; // i.e.  Dprime
+		$('#ldproxy-genome').html("View D' data in UCSC Genome Browser");
+		//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
+	}
+
+	var ldproxyInputs = {
+		var: $('#ldproxy-snp').val(),
+		pop: population.join('+'),
+		reference: Math.floor(Math.random() * (99999 - 10000 + 1)),
+		genome_build: genomeBuild,
+		r2_d: r2_d,
+		window: windowSize,
+		collapseTranscript: $('#proxy_collapse_transcripts').hasClass('active'),
+		annotate: document.querySelector('input[name="ldproxy_options"]:checked')
+			.value,
+	};
+
+	updateHistoryURL(id, ldproxyInputs);
+	//console.log(ldproxyInputs)
+	//console.log(location.hostname);
+
+	var proxy_build = genomeBuild == 'grch37' ? 'hg19' : 'hg38';
+	$('#ldproxy-genome').attr(
+		'href',
+		'https://genome.ucsc.edu/cgi-bin/hgTracks?db=' +
+			proxy_build +
+			'&hgt.customText=http://' +
+			location.hostname +
+			'/LDlinkRestWeb/tmp/track' +
+			ldproxyInputs.reference +
+			'.txt'
+	);
+
+	$('#ldproxy-results-link').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/proxy' + ldproxyInputs.reference + '.txt'
+	);
+	var url = restServerUrl + '/ldproxy';
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldproxyInputs,
+	});
+	ajaxRequest.success(function (data) {
+		// if (displayError(id, data) == false) {
+		//     $('#' + id + '-progress-container').hide();
+		//     $('#ldproxy-bokeh-graph').empty().append(data);
+		//     $('#' + id + '-results-container').show();
+		//     getLDProxyResults('proxy'+ldproxyInputs.reference+".json");
+		// }
+		// $("#"+id+"-loading").hide();
+
+		// create bokeh object with output_backend=canvas from svg
+		var dataString = data;
+		var dataCanvas = new Object([dataString]);
+
+		var jsonObjCanvas;
+		if (typeof dataCanvas == 'string') {
+			jsonObjCanvas = JSON.parse(dataCanvas);
+		} else {
+			jsonObjCanvas = dataCanvas;
+		}
+
+		// display graph if no errors
+		if (displayError(id, jsonObjCanvas) == false) {
+			switch (genomeBuild) {
+				case 'grch37':
+					$('.' + id + '-position-genome-build-header').text('GRCh37');
+					break;
+				case 'grch38':
+					$('.' + id + '-position-genome-build-header').text('GRCh38');
+					break;
+				case 'grch38_high_coverage':
+					$('.' + id + '-position-genome-build-header').text(
+						'GRCh38 High Coverage'
+					);
+					break;
+			}
+
+			$('#ldproxy-bokeh-graph').empty().append(dataCanvas);
+
+			// place Download PDF button
+			$('#' + id + '-export-dropdown')
+				.empty()
+				.prepend(
+					'<div class="dropdown pull-right"><button class="btn btn-default dropdown-toggle" type="button" id="ldproxy-menu1" data-toggle="dropdown" disabled>Exporting Plot <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span></button><ul class="dropdown-menu " role="menu" aria-labelledby="menu1" style="overflow: hidden;"><li role="presentation"><a role="menuitem" id="ldproxy-downloadSVG" class="text-center" tabindex="-1" >SVG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadPDF" class="text-center" tabindex="-1" >PDF</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadPNG" class="text-center" tabindex="-1" >PNG</a></li><li role="presentation" class="divider"></li><li role="presentation"><a role="menuitem" id="ldproxy-downloadJPEG" class="text-center" tabindex="-1" >JPEG</a></li></ul></div>'
+				);
+			$('#ldproxy-downloadSVG').click(function (e) {
+				e.preventDefault();
+				var proxy_plot =
+					'/LDlinkRestWeb/tmp/proxy_plot_' + ldproxyInputs.reference + '.svg';
+				window.open(proxy_plot, '_blank');
+			});
+			$('#ldproxy-downloadPDF').click(function (e) {
+				e.preventDefault();
+				var proxy_plot =
+					'/LDlinkRestWeb/tmp/proxy_plot_' + ldproxyInputs.reference + '.pdf';
+				window.open(proxy_plot, '_blank');
+			});
+			$('#ldproxy-downloadPNG').click(function (e) {
+				e.preventDefault();
+				var proxy_plot =
+					'/LDlinkRestWeb/tmp/proxy_plot_' + ldproxyInputs.reference + '.png';
+				window.open(proxy_plot, '_blank');
+			});
+			$('#ldproxy-downloadJPEG').click(function (e) {
+				e.preventDefault();
+				var proxy_plot =
+					'/LDlinkRestWeb/tmp/proxy_plot_' + ldproxyInputs.reference + '.jpeg';
+				window.open(proxy_plot, '_blank');
+			});
+
+			// enable button once .svg file is generated from subprocess
+			var fileURL =
+				'/LDlinkRestWeb/tmp/proxy_plot_' + ldproxyInputs.reference + '.jpeg';
+			checkFile(id, fileURL, 180);
+
+			$('#' + id + '-results-container').show();
+			getLDProxyResults('proxy' + ldproxyInputs.reference + '.json');
+		} else {
+			displayError(id, dataCanvas);
+		}
+		$('#' + id + '-loading').hide();
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+		setTimeout(function () {
+			var checkbox = $('.bk-toolbar-inspector').children().first();
+			$(checkbox).attr('id', 'hover');
+			$(checkbox).append(
+				'<label for="hover" class="sr-only">Hover Tool</label>'
+			);
+		}, 100);
+	});
 }
 
 function hideLoadingIcon(ajaxRequest, id) {
-    ajaxRequest.done(function(msg) {
-        //hide loading icon
-        $('#'+id+"-loading").hide();
-    });
+	ajaxRequest.done(function (msg) {
+		//hide loading icon
+		$('#' + id + '-loading').hide();
+	});
 }
 
 function getLDProxyResults(jsonfile) {
-    var id = "ldproxy";
-    var url = "/LDlinkRestWeb/tmp/"+jsonfile;
-    //console.info("Here is the LOG file");
-    //console.log(url);
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url
-    });
-    ajaxRequest.success(function(data) {
-        //catch error and warning in json
-        if (displayError(id, data) == false) {
-            RefreshTable('#new-ldproxy', data);
-        }
-
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldproxy';
+	var url = '/LDlinkRestWeb/tmp/' + jsonfile;
+	//console.info("Here is the LOG file");
+	//console.log(url);
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+	});
+	ajaxRequest.success(function (data) {
+		//catch error and warning in json
+		if (displayError(id, data) == false) {
+			RefreshTable('#new-ldproxy', data);
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function getLDAssocResults(jsonfile) {
-    var id = "ldassoc";
-    var url = "/LDlinkRestWeb/tmp/"+jsonfile;
-    //console.info("Here is the LOG file");
-    //console.log(url);
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url
-    });
-    ajaxRequest.success(function(data) {
-        //catch error and warning in json
-        // console.warn("HERE IS THE ldassoc data");
-        // console.dir(data);
-        if (displayError(id, data) == false) {
-            RefreshTable('#new-ldassoc', data);
-            $("#ldassoc-namespace").empty();
-            $("#ldassoc-namespace").append(
-                $("<div>").append("namespace("+
-                    JSON.stringify(data.report.namespace)
-                    +")"
-                )
-            );
-            $("#ldassoc-namespace").append(
-                $("<div>").append("region = "+data.report.region)
-            );
-            $("#ldassoc-stats").empty().append(
-                $("<li>").append("Number of Individuals: <b>"+data.report.statistics.individuals+"</b>")
-            );
-            $("#ldassoc-stats").append(
-                $("<li>").append("Variants in Region: <b>"+data.report.statistics.in_region+"</b>")
-            );
-            $("#ldassoc-stats").append(
-                $("<li>").append("Run time: <b>"+Number(data.report.statistics.runtime).toFixed(2)+"</b> seconds")
-            );
-            //Adjust links
-            if($('#assoc-matrix-color-r2').hasClass('active')) {
-                $('#ldassoc-genome').html("View R<sup>2</sup> data in UCSC Genome Browser");
-                //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
-            } else {
-                $('#ldassoc-genome').html("View D' data in UCSC Genome Browser");
-                //$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
-            }
-            //transcript flag?
-            if($('#assoc-transcript').hasClass('active')) {
-                //Yes
-
-            } else {
-                //No
-            }
-            //annotate flag?
-            if($('#assoc-annotate').hasClass('active')) {
-                //Yes
-
-            } else {
-                //No
-
-            }
-
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldassoc';
+	var url = '/LDlinkRestWeb/tmp/' + jsonfile;
+	//console.info("Here is the LOG file");
+	//console.log(url);
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+	});
+	ajaxRequest.success(function (data) {
+		//catch error and warning in json
+		// console.warn("HERE IS THE ldassoc data");
+		// console.dir(data);
+		if (displayError(id, data) == false) {
+			RefreshTable('#new-ldassoc', data);
+			$('#ldassoc-namespace').empty();
+			$('#ldassoc-namespace').append(
+				$('<div>').append(
+					'namespace(' + JSON.stringify(data.report.namespace) + ')'
+				)
+			);
+			$('#ldassoc-namespace').append(
+				$('<div>').append('region = ' + data.report.region)
+			);
+			$('#ldassoc-stats')
+				.empty()
+				.append(
+					$('<li>').append(
+						'Number of Individuals: <b>' +
+							data.report.statistics.individuals +
+							'</b>'
+					)
+				);
+			$('#ldassoc-stats').append(
+				$('<li>').append(
+					'Variants in Region: <b>' + data.report.statistics.in_region + '</b>'
+				)
+			);
+			$('#ldassoc-stats').append(
+				$('<li>').append(
+					'Run time: <b>' +
+						Number(data.report.statistics.runtime).toFixed(2) +
+						'</b> seconds'
+				)
+			);
+			//Adjust links
+			if ($('#assoc-matrix-color-r2').hasClass('active')) {
+				$('#ldassoc-genome').html(
+					'View R<sup>2</sup> data in UCSC Genome Browser'
+				);
+				//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_R2.png');
+			} else {
+				$('#ldassoc-genome').html("View D' data in UCSC Genome Browser");
+				//$("#ldmatrix-legend").attr('src', 'LDmatrix_legend_Dprime.png');
+			}
+			//transcript flag?
+			if ($('#assoc-transcript').hasClass('active')) {
+				//Yes
+			} else {
+				//No
+			}
+			//annotate flag?
+			if ($('#assoc-annotate').hasClass('active')) {
+				//Yes
+			} else {
+				//No
+			}
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function getLDmatrixResults(jsonfile, request) {
-    var id = "ldmatrix";
-    var url = "/LDlinkRestWeb/tmp/matrix"+jsonfile;
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url
-    });
-
-    ajaxRequest.success(function(data) {
-        //catch error and warning in json
-        if (displayError(id, data) == false) {
-            addLDMatrixHyperLinks(request);
-            $('#'+id+"-download-links").show();
-        }
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-    });
+	var id = 'ldmatrix';
+	var url = '/LDlinkRestWeb/tmp/matrix' + jsonfile;
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+	});
+
+	ajaxRequest.success(function (data) {
+		//catch error and warning in json
+		if (displayError(id, data) == false) {
+			addLDMatrixHyperLinks(request);
+			$('#' + id + '-download-links').show();
+		}
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {});
 }
 
 function updateHistoryURL(id, inputs) {
-    //console.log('updateHistoryURL: id:'+id+' inputs:'+inputs);
-    //Update url with new vars
-    var params = $.extend({}, inputs);
-    delete params.reference;
-    if(params.pop) {
-        var population;
-        var totalPopulations;
-        population =  $('#'+id+'-population-codes').val();
-        params.pop = population.join("+");
-    }
-
-    params["tab"] = id;
-    var recursiveEncoded = $.param( params );
-    //console.log(recursiveEncoded);
-    window.history.pushState({},'', "?"+ recursiveEncoded);
-    $("#"+id+"-tab-anchor").attr("data-url-params", recursiveEncoded);
-
-    //console.log(JSON.stringify(params.pop));
-
+	//console.log('updateHistoryURL: id:'+id+' inputs:'+inputs);
+	//Update url with new vars
+	var params = $.extend({}, inputs);
+	delete params.reference;
+	if (params.pop) {
+		var population;
+		var totalPopulations;
+		population = $('#' + id + '-population-codes').val();
+		params.pop = population.join('+');
+	}
+
+	params['tab'] = id;
+	var recursiveEncoded = $.param(params);
+	//console.log(recursiveEncoded);
+	window.history.pushState({}, '', '?' + recursiveEncoded);
+	$('#' + id + '-tab-anchor').attr('data-url-params', recursiveEncoded);
+
+	//console.log(JSON.stringify(params.pop));
 }
 
 function updateLDpair() {
-    var id = 'ldpair';
-    var $btn = $('#' + id).button('loading');
-
-    var population = getPopulationCodes(id+'-population-codes');
-
-    //console.log("LD Pair");
-    //console.log('population');
-    //console.dir(population);
-    var ldpairInputs = {
-        var1 : $('#ldpair-snp1').val(),
-        var2 : $('#ldpair-snp2').val(),
-        pop : population.join("+"),
-        genome_build: genomeBuild
-    };
-    //console.log("ldpairInputs");
-    //console.dir(ldpairInputs);
-
-    updateHistoryURL(id, ldpairInputs);
-
-    var url = restServerUrl + "/ldpair";
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url,
-        data : ldpairInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        if (displayError(id, data[0]) == false) {
-            ko.mapping.fromJS(data[0], ldpairModel);
-            $('#' + id + '-results-container').show();
-            addLDpairHyperLinks(data[0]);
-        }
-        $("#ldpair_results").text("Download Results");
-        $('#ldpair_results').css("text-decoration", "underline");
-        $("#ldpair_results").attr("href", "/LDlinkRestWeb/tmp/LDpair_" + data[0]['request'] + ".txt");
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldpair';
+	var $btn = $('#' + id).button('loading');
+
+	var population = getPopulationCodes(id + '-population-codes');
+
+	//console.log("LD Pair");
+	//console.log('population');
+	//console.dir(population);
+	var ldpairInputs = {
+		var1: $('#ldpair-snp1').val(),
+		var2: $('#ldpair-snp2').val(),
+		pop: population.join('+'),
+		genome_build: genomeBuild,
+	};
+	//console.log("ldpairInputs");
+	//console.dir(ldpairInputs);
+
+	updateHistoryURL(id, ldpairInputs);
+
+	var url = restServerUrl + '/ldpair';
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldpairInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		if (displayError(id, data[0]) == false) {
+			ko.mapping.fromJS(data[0], ldpairModel);
+			$('#' + id + '-results-container').show();
+			addLDpairHyperLinks(data[0]);
+		}
+		$('#ldpair_results').text('Download Results');
+		$('#ldpair_results').css('text-decoration', 'underline');
+		$('#ldpair_results').attr(
+			'href',
+			'/LDlinkRestWeb/tmp/LDpair_' + data[0]['request'] + '.txt'
+		);
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 var map1, map2, map3;
 // Initialize and add the map
 function initMap() {
-    var initOptions = {
-        zoom: 2, 
-        center: {
-            lat: 30, 
-            lng: 0
-        },
-        controlSize: 24
-        // disableDefaultUI: true
-        // streetViewControl: false
-    };
-    map1 = new google.maps.Map(document.getElementById('map1'), initOptions);
-    map2 = new google.maps.Map(document.getElementById('map2'), initOptions);
-    map3 = new google.maps.Map(document.getElementById('map3'), initOptions);
-
-    var LDlegend = document.getElementById('ldpop-ld-legend');
-    var MAFlegend1 = document.getElementById('ldpop-maf-legend1');
-    var MAFlegend2 = document.getElementById('ldpop-maf-legend2');
-    map1.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(LDlegend);
-    map2.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(MAFlegend1);
-    map3.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(MAFlegend2);
-
-    // add alt text to maps
-    google.maps.event.addListener(map1, 'tilesloaded', function() {
-        var images1 = document.querySelectorAll('#map1 img');
-        images1.forEach(function(image1) {
-            image1.alt = "Google Maps API control";
-        });
-    });
-    google.maps.event.addListener(map2, 'tilesloaded', function() {
-        var images2 = document.querySelectorAll('#map2 img');
-        images2.forEach(function(image2) {
-            image2.alt = "Google Maps API control";
-        });
-    });
-    google.maps.event.addListener(map3, 'tilesloaded', function() {
-        var images3 = document.querySelectorAll('#map3 img');
-        images3.forEach(function(image3) {
-            image3.alt = "Google Maps API control";
-        });
-    });
-
-    // sample marker test google maps api local
-    // var myLatLng = {lat: -25.363, lng: 131.044};
-    // let icon = {
-    //     path: "M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z",
-    //     strokeColor: "black",
-    //     fillColor: "red",
-    //     fillOpacity: 1,
-    //     scale: .85,
-    //     labelOrigin: new google.maps.Point(0, -30)
-    // }
-    // var marker = new google.maps.Marker({
-    //     position: myLatLng,
-    //     map: map1,
-    //     icon: icon,
-    //     title: 'Hello World!',
-    //     label: {
-    //         text: "GWK",
-    //         fontSize: "12px"
-    //     }
-    // });
+	var initOptions = {
+		zoom: 2,
+		center: {
+			lat: 30,
+			lng: 0,
+		},
+		controlSize: 24,
+		// disableDefaultUI: true
+		// streetViewControl: false
+	};
+	map1 = new google.maps.Map(document.getElementById('map1'), initOptions);
+	map2 = new google.maps.Map(document.getElementById('map2'), initOptions);
+	map3 = new google.maps.Map(document.getElementById('map3'), initOptions);
+
+	var LDlegend = document.getElementById('ldpop-ld-legend');
+	var MAFlegend1 = document.getElementById('ldpop-maf-legend1');
+	var MAFlegend2 = document.getElementById('ldpop-maf-legend2');
+	map1.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(LDlegend);
+	map2.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(MAFlegend1);
+	map3.controls[google.maps.ControlPosition.BOTTOM_LEFT].push(MAFlegend2);
+
+	// add alt text to maps
+	google.maps.event.addListener(map1, 'tilesloaded', function () {
+		var images1 = document.querySelectorAll('#map1 img');
+		images1.forEach(function (image1) {
+			image1.alt = 'Google Maps API control';
+		});
+	});
+	google.maps.event.addListener(map2, 'tilesloaded', function () {
+		var images2 = document.querySelectorAll('#map2 img');
+		images2.forEach(function (image2) {
+			image2.alt = 'Google Maps API control';
+		});
+	});
+	google.maps.event.addListener(map3, 'tilesloaded', function () {
+		var images3 = document.querySelectorAll('#map3 img');
+		images3.forEach(function (image3) {
+			image3.alt = 'Google Maps API control';
+		});
+	});
+
+	// sample marker test google maps api local
+	// var myLatLng = {lat: -25.363, lng: 131.044};
+	// let icon = {
+	//     path: "M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z",
+	//     strokeColor: "black",
+	//     fillColor: "red",
+	//     fillOpacity: 1,
+	//     scale: .85,
+	//     labelOrigin: new google.maps.Point(0, -30)
+	// }
+	// var marker = new google.maps.Marker({
+	//     position: myLatLng,
+	//     map: map1,
+	//     icon: icon,
+	//     title: 'Hello World!',
+	//     label: {
+	//         text: "GWK",
+	//         fontSize: "12px"
+	//     }
+	// });
 }
 
 function setLDColor(LD) {
-    var LDColorData = {
-        0: "#FFFFFF",
-        0.0 : "#FFFFFF",
-        0.1 : "#FBE6E6",
-        0.2 : "#F8D3D2",
-        0.3 : "#F4B5B4",
-        0.4 : "#F19E9C",
-        0.5 : "#EF8683",
-        0.6 : "#EC706B",
-        0.7 : "#EB5A54",
-        0.8 : "#EB483F",
-        0.9 : "#E9392D",
-        1.0 : "#E9392D",
-        1: "#E9392D"
-    };
-    // round r2 to 1 decimal place and return color
-    var round_LD = Math.round(LD * 10 ) / 10;
-    return LDColorData[round_LD];
+	var LDColorData = {
+		0: '#FFFFFF',
+		0.0: '#FFFFFF',
+		0.1: '#FBE6E6',
+		0.2: '#F8D3D2',
+		0.3: '#F4B5B4',
+		0.4: '#F19E9C',
+		0.5: '#EF8683',
+		0.6: '#EC706B',
+		0.7: '#EB5A54',
+		0.8: '#EB483F',
+		0.9: '#E9392D',
+		1.0: '#E9392D',
+		1: '#E9392D',
+	};
+	// round r2 to 1 decimal place and return color
+	var round_LD = Math.round(LD * 10) / 10;
+	return LDColorData[round_LD];
 }
 
 function colorMarkerLD(LD, location) {
-    // console.log("LD", LD);
-    var r2 = location[7];
-    var dprime = location[8];
-    // console.log("R2: ", r2);
-    // console.log("D\': ", dprime);
-    if (LD == "r2") {
-        if (r2 == "NA") {
-            return "#E9F3F9";
-        } else {
-            return setLDColor(r2);
-        }
-    } else {
-        if (dprime == "NA") {
-            return "#E9F3F9";
-        } else {
-            return setLDColor(dprime);
-        }
-    }
+	// console.log("LD", LD);
+	var r2 = location[7];
+	var dprime = location[8];
+	// console.log("R2: ", r2);
+	// console.log("D\': ", dprime);
+	if (LD == 'r2') {
+		if (r2 == 'NA') {
+			return '#E9F3F9';
+		} else {
+			return setLDColor(r2);
+		}
+	} else {
+		if (dprime == 'NA') {
+			return '#E9F3F9';
+		} else {
+			return setLDColor(dprime);
+		}
+	}
 }
 
 function getMinorAllele(variantIndex, locations) {
-    // console.log(variantIndex);
-    var alleles = locations[0][variantIndex].replace(/[\s\%]/g, '').split(/[\,\:]/);
-    var allele1 = alleles[0];
-    var allele2 = alleles[2];
-    var allele1PopSize = 0;
-    var allele2PopSize = 0;
-    var pop_groups = ["ALL", "AFR", "AMR", "EAS", "EUR", "SAS"];
-    for (i = 0; i < locations.length; i++) {
-        if (!pop_groups.includes(locations[i][0])) {
-            // console.log(locations[i][0]);
-            let alleleData = locations[i][variantIndex].replace(/[\s\%]/g, '').split(/[\,\:]/);
-            let allele1Freq = parseFloat(alleleData[1]);
-            let allele2Freq = parseFloat(alleleData[3]);
-            if (allele1Freq == allele2Freq) {
-                allele1PopSize = allele1PopSize + locations[i][1];
-                allele2PopSize = allele2PopSize + locations[i][1];
-            } else if (allele1Freq < allele2Freq) {
-                allele1PopSize = allele1PopSize + locations[i][1];
-            } else {
-                allele2PopSize = allele2PopSize + locations[i][1];
-            }
-        }
-    }
-    // console.log("Allele 1: ", allele1);
-    // console.log("Allele 1 Pop Size: ", allele1PopSize);
-    // console.log("Allele 2: ", allele2);
-    // console.log("Allele 2 Pop Size: ", allele2PopSize);
-    if (allele1PopSize == allele2PopSize) {
-        if (allele1 < allele2) {
-            return allele1;
-        } else {
-            return allele2;
-        }
-    } else if (allele1PopSize > allele2PopSize) {
-        return allele1;
-    } else {
-        return allele2;
-    }
+	// console.log(variantIndex);
+	var alleles = locations[0][variantIndex]
+		.replace(/[\s\%]/g, '')
+		.split(/[\,\:]/);
+	var allele1 = alleles[0];
+	var allele2 = alleles[2];
+	var allele1PopSize = 0;
+	var allele2PopSize = 0;
+	var pop_groups = ['ALL', 'AFR', 'AMR', 'EAS', 'EUR', 'SAS'];
+	for (i = 0; i < locations.length; i++) {
+		if (!pop_groups.includes(locations[i][0])) {
+			// console.log(locations[i][0]);
+			let alleleData = locations[i][variantIndex]
+				.replace(/[\s\%]/g, '')
+				.split(/[\,\:]/);
+			let allele1Freq = parseFloat(alleleData[1]);
+			let allele2Freq = parseFloat(alleleData[3]);
+			if (allele1Freq == allele2Freq) {
+				allele1PopSize = allele1PopSize + locations[i][1];
+				allele2PopSize = allele2PopSize + locations[i][1];
+			} else if (allele1Freq < allele2Freq) {
+				allele1PopSize = allele1PopSize + locations[i][1];
+			} else {
+				allele2PopSize = allele2PopSize + locations[i][1];
+			}
+		}
+	}
+	// console.log("Allele 1: ", allele1);
+	// console.log("Allele 1 Pop Size: ", allele1PopSize);
+	// console.log("Allele 2: ", allele2);
+	// console.log("Allele 2 Pop Size: ", allele2PopSize);
+	if (allele1PopSize == allele2PopSize) {
+		if (allele1 < allele2) {
+			return allele1;
+		} else {
+			return allele2;
+		}
+	} else if (allele1PopSize > allele2PopSize) {
+		return allele1;
+	} else {
+		return allele2;
+	}
 }
 
 function setMAFColor(MAF) {
-    var MAFColorData = {
-        0: "#FFFFFF",
-        0.0 : "#FFFFFF",
-        0.1 : "#E5E7FD",
-        0.2 : "#D0D4FB",
-        0.3 : "#B3BAFA",
-        0.4 : "#9AA3F8",
-        0.5 : "#828EF7",
-        0.6 : "#6877F6",
-        0.7 : "#4E60F5",
-        0.8 : "#354CF5",
-        0.9 : "#1B37F3",
-        1.0 : "#1B37F3",
-        1: "#1B37F3"
-    };
-    // round MAF to 1 decimal place and return color
-    var round_MAF = Math.round(MAF * 10 ) / 10;
-    return MAFColorData[round_MAF];
+	var MAFColorData = {
+		0: '#FFFFFF',
+		0.0: '#FFFFFF',
+		0.1: '#E5E7FD',
+		0.2: '#D0D4FB',
+		0.3: '#B3BAFA',
+		0.4: '#9AA3F8',
+		0.5: '#828EF7',
+		0.6: '#6877F6',
+		0.7: '#4E60F5',
+		0.8: '#354CF5',
+		0.9: '#1B37F3',
+		1.0: '#1B37F3',
+		1: '#1B37F3',
+	};
+	// round MAF to 1 decimal place and return color
+	var round_MAF = Math.round(MAF * 10) / 10;
+	return MAFColorData[round_MAF];
 }
 
 function colorMarkerMAF(minorAllele, location) {
-    // console.log("Minor Allele: ", minorAllele);
-    var alleleData = location[5];
-    var alleleData = alleleData.replace(/[\s\%]/g, '').split(/[\,\:]/);
-    var alleleDataHash = {};
-    alleleDataHash[alleleData[0]] = parseFloat(alleleData[1]);
-    alleleDataHash[alleleData[2]] = parseFloat(alleleData[3]);
-    var MAF = alleleDataHash[minorAllele] / 100.0;
-    return setMAFColor(MAF);
+	// console.log("Minor Allele: ", minorAllele);
+	var alleleData = location[5];
+	var alleleData = alleleData.replace(/[\s\%]/g, '').split(/[\,\:]/);
+	var alleleDataHash = {};
+	alleleDataHash[alleleData[0]] = parseFloat(alleleData[1]);
+	alleleDataHash[alleleData[2]] = parseFloat(alleleData[3]);
+	var MAF = alleleDataHash[minorAllele] / 100.0;
+	return setMAFColor(MAF);
 }
 
 var markersArray = [];
 function clearOverlays() {
-    for (var i = 0; i < markersArray.length; i++ ) {
-        markersArray[i].setMap(null);
-    }
-    markersArray.length = 0;
+	for (var i = 0; i < markersArray.length; i++) {
+		markersArray[i].setMap(null);
+	}
+	markersArray.length = 0;
 }
 
 function resetMarkerZIndex() {
-    var count = 0;
-    for (var i = 0; i < markersArray.length; i++ ) {
-        count = count + 1;
-        markersArray[i].setZIndex(count);
-    }
+	var count = 0;
+	for (var i = 0; i < markersArray.length; i++) {
+		count = count + 1;
+		markersArray[i].setZIndex(count);
+	}
 }
 
 function addMarkers(data) {
-    var locations = data.locations;
-    var rs1MinorAllele = getMinorAllele(2, data.aaData);
-    var rs2MinorAllele = getMinorAllele(3, data.aaData);
-    // console.log("Minor Allele rs#1: ", rs1MinorAllele);
-    // console.log("Minor Allele rs#2: ", rs2MinorAllele);
-    // rs#1 Frequencies map
-    var map1_infowindow = new google.maps.InfoWindow();
-    var map1_marker, map1_i;
-    for (map1_i = 0; map1_i < locations.rs1_rs2_LD_map.length; map1_i++) {
-        let icon = {
-            path: "M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z",
-            strokeColor: "black",
-            fillColor: colorMarkerLD(data.inputs.LD, locations.rs1_rs2_LD_map[map1_i]),
-            fillOpacity: 1,
-            scale: .85,
-            labelOrigin: new google.maps.Point(0, -30)
-        }
-        map1_marker = new google.maps.Marker({
-            position: {
-                lat: locations.rs1_rs2_LD_map[map1_i][3], 
-                lng: locations.rs1_rs2_LD_map[map1_i][4]
-            }, 
-            icon: icon,
-            map: map1,
-            label: {
-                text: locations.rs1_rs2_LD_map[map1_i][0],
-                fontSize: "12px"
-            },
-            title: "(" + locations.rs1_rs2_LD_map[map1_i][0] + ") " + locations.rs1_rs2_LD_map[map1_i][1]
-        });
-        markersArray.push(map1_marker);
-        google.maps.event.addListener(map1_marker, 'click', (function(map1_marker, map1_i) {
-            return function() {
-                var contentString = '<div><b>(' + locations.rs1_rs2_LD_map[map1_i][0] + ') - ' + locations.rs1_rs2_LD_map[map1_i][1] + '</b><hr style="margin-top: 5px; margin-bottom: 5px;">' + 
-                    '<b>' + data.inputs.rs1 + '</b>: ' + locations.rs1_rs2_LD_map[map1_i][5] + '<br>' + 
-                    '<b>' + data.inputs.rs2 + '</b>: ' + locations.rs1_rs2_LD_map[map1_i][6] + '<br>' + 
-                    '<b>R<sup>2</sup></b>: ' + locations.rs1_rs2_LD_map[map1_i][7] + '<br>' + 
-                    '<b>D\'</b>: ' + locations.rs1_rs2_LD_map[map1_i][8] + '</div>';
-                map1_infowindow.setContent(contentString);
-                map1_infowindow.open(map1, map1_marker);
-                resetMarkerZIndex();
-                map1_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
-            }
-        })(map1_marker, map1_i));
-    }
-    // rs#2 Frequencies map
-    var map2_infowindow = new google.maps.InfoWindow();
-    var map2_marker, map2_i;
-    for (map2_i = 0; map2_i < locations.rs1_map.length; map2_i++) {
-        let icon = {
-            path: "M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z",
-            strokeColor: "black",
-            fillColor: colorMarkerMAF(rs1MinorAllele, locations.rs1_map[map2_i]),
-            fillOpacity: 1,
-            scale: .85,
-            labelOrigin: new google.maps.Point(0, -30)
-        }
-        map2_marker = new google.maps.Marker({
-            position: {
-                lat: locations.rs1_map[map2_i][3], 
-                lng: locations.rs1_map[map2_i][4]
-            },
-            icon: icon,
-            map: map2,
-            label: {
-                text: locations.rs1_map[map2_i][0],
-                fontSize: "12px"
-            },
-            title: "(" + locations.rs1_map[map2_i][0] + ") " + locations.rs1_map[map2_i][1]
-        });
-        markersArray.push(map2_marker);
-        google.maps.event.addListener(map2_marker, 'click', (function(map2_marker, map2_i) {
-            return function() {
-                var contentString = '<div><b>(' + locations.rs1_map[map2_i][0] + ') - ' + locations.rs1_map[map2_i][1] + '</b><hr style="margin-top: 5px; margin-bottom: 5px;">' + 
-                    locations.rs1_map[map2_i][5] + '</div>';
-                map2_infowindow.setContent(contentString);
-                map2_infowindow.open(map2, map2_marker);
-                resetMarkerZIndex();
-                map2_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
-            }
-        })(map2_marker, map2_i));
-    }
-    // rs#1-rs#2 LD map
-    var map3_infowindow = new google.maps.InfoWindow();
-    var map3_marker, map3_i;
-    for (map3_i = 0; map3_i < locations.rs2_map.length; map3_i++) {
-        let icon = {
-            path: "M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z",
-            strokeColor: "black",
-            fillColor: colorMarkerMAF(rs2MinorAllele, locations.rs2_map[map3_i]),
-            fillOpacity: 1,
-            scale: .85,
-            labelOrigin: new google.maps.Point(0, -30)
-        }
-        map3_marker = new google.maps.Marker({
-            position: {
-                lat: locations.rs2_map[map3_i][3], 
-                lng: locations.rs2_map[map3_i][4]
-            }, 
-            icon: icon,
-            map: map3,
-            label: {
-                text: locations.rs2_map[map3_i][0],
-                fontSize: "12px"
-            },
-            title: "(" + locations.rs2_map[map3_i][0] + ") " + locations.rs2_map[map3_i][1]
-        });
-        markersArray.push(map3_marker);
-        google.maps.event.addListener(map3_marker, 'click', (function(map3_marker, map3_i) {
-            return function() {
-                var contentString = '<div><b>(' + locations.rs2_map[map3_i][0] + ') - ' + locations.rs2_map[map3_i][1] + '</b><hr style="margin-top: 5px; margin-bottom: 5px;">' + 
-                    locations.rs2_map[map3_i][5] + '</div>';
-                map3_infowindow.setContent(contentString);
-                map3_infowindow.open(map3, map3_marker);
-                resetMarkerZIndex();
-                map3_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
-            }
-        })(map3_marker, map3_i));
-    }
+	var locations = data.locations;
+	var rs1MinorAllele = getMinorAllele(2, data.aaData);
+	var rs2MinorAllele = getMinorAllele(3, data.aaData);
+	// console.log("Minor Allele rs#1: ", rs1MinorAllele);
+	// console.log("Minor Allele rs#2: ", rs2MinorAllele);
+	// rs#1 Frequencies map
+	var map1_infowindow = new google.maps.InfoWindow();
+	var map1_marker, map1_i;
+	for (map1_i = 0; map1_i < locations.rs1_rs2_LD_map.length; map1_i++) {
+		let icon = {
+			path: 'M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z',
+			strokeColor: 'black',
+			fillColor: colorMarkerLD(
+				data.inputs.LD,
+				locations.rs1_rs2_LD_map[map1_i]
+			),
+			fillOpacity: 1,
+			scale: 0.85,
+			labelOrigin: new google.maps.Point(0, -30),
+		};
+		map1_marker = new google.maps.Marker({
+			position: {
+				lat: locations.rs1_rs2_LD_map[map1_i][3],
+				lng: locations.rs1_rs2_LD_map[map1_i][4],
+			},
+			icon: icon,
+			map: map1,
+			label: {
+				text: locations.rs1_rs2_LD_map[map1_i][0],
+				fontSize: '12px',
+			},
+			title:
+				'(' +
+				locations.rs1_rs2_LD_map[map1_i][0] +
+				') ' +
+				locations.rs1_rs2_LD_map[map1_i][1],
+		});
+		markersArray.push(map1_marker);
+		google.maps.event.addListener(
+			map1_marker,
+			'click',
+			(function (map1_marker, map1_i) {
+				return function () {
+					var contentString =
+						'<div><b>(' +
+						locations.rs1_rs2_LD_map[map1_i][0] +
+						') - ' +
+						locations.rs1_rs2_LD_map[map1_i][1] +
+						'</b><hr style="margin-top: 5px; margin-bottom: 5px;">' +
+						'<b>' +
+						data.inputs.rs1 +
+						'</b>: ' +
+						locations.rs1_rs2_LD_map[map1_i][5] +
+						'<br>' +
+						'<b>' +
+						data.inputs.rs2 +
+						'</b>: ' +
+						locations.rs1_rs2_LD_map[map1_i][6] +
+						'<br>' +
+						'<b>R<sup>2</sup></b>: ' +
+						locations.rs1_rs2_LD_map[map1_i][7] +
+						'<br>' +
+						"<b>D'</b>: " +
+						locations.rs1_rs2_LD_map[map1_i][8] +
+						'</div>';
+					map1_infowindow.setContent(contentString);
+					map1_infowindow.open(map1, map1_marker);
+					resetMarkerZIndex();
+					map1_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
+				};
+			})(map1_marker, map1_i)
+		);
+	}
+	// rs#2 Frequencies map
+	var map2_infowindow = new google.maps.InfoWindow();
+	var map2_marker, map2_i;
+	for (map2_i = 0; map2_i < locations.rs1_map.length; map2_i++) {
+		let icon = {
+			path: 'M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z',
+			strokeColor: 'black',
+			fillColor: colorMarkerMAF(rs1MinorAllele, locations.rs1_map[map2_i]),
+			fillOpacity: 1,
+			scale: 0.85,
+			labelOrigin: new google.maps.Point(0, -30),
+		};
+		map2_marker = new google.maps.Marker({
+			position: {
+				lat: locations.rs1_map[map2_i][3],
+				lng: locations.rs1_map[map2_i][4],
+			},
+			icon: icon,
+			map: map2,
+			label: {
+				text: locations.rs1_map[map2_i][0],
+				fontSize: '12px',
+			},
+			title:
+				'(' +
+				locations.rs1_map[map2_i][0] +
+				') ' +
+				locations.rs1_map[map2_i][1],
+		});
+		markersArray.push(map2_marker);
+		google.maps.event.addListener(
+			map2_marker,
+			'click',
+			(function (map2_marker, map2_i) {
+				return function () {
+					var contentString =
+						'<div><b>(' +
+						locations.rs1_map[map2_i][0] +
+						') - ' +
+						locations.rs1_map[map2_i][1] +
+						'</b><hr style="margin-top: 5px; margin-bottom: 5px;">' +
+						locations.rs1_map[map2_i][5] +
+						'</div>';
+					map2_infowindow.setContent(contentString);
+					map2_infowindow.open(map2, map2_marker);
+					resetMarkerZIndex();
+					map2_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
+				};
+			})(map2_marker, map2_i)
+		);
+	}
+	// rs#1-rs#2 LD map
+	var map3_infowindow = new google.maps.InfoWindow();
+	var map3_marker, map3_i;
+	for (map3_i = 0; map3_i < locations.rs2_map.length; map3_i++) {
+		let icon = {
+			path: 'M0-48c-9.8 0-17.7 7.8-17.7 17.4 0 15.5 17.7 30.6 17.7 30.6s17.7-15.4 17.7-30.6c0-9.6-7.9-17.4-17.7-17.4z',
+			strokeColor: 'black',
+			fillColor: colorMarkerMAF(rs2MinorAllele, locations.rs2_map[map3_i]),
+			fillOpacity: 1,
+			scale: 0.85,
+			labelOrigin: new google.maps.Point(0, -30),
+		};
+		map3_marker = new google.maps.Marker({
+			position: {
+				lat: locations.rs2_map[map3_i][3],
+				lng: locations.rs2_map[map3_i][4],
+			},
+			icon: icon,
+			map: map3,
+			label: {
+				text: locations.rs2_map[map3_i][0],
+				fontSize: '12px',
+			},
+			title:
+				'(' +
+				locations.rs2_map[map3_i][0] +
+				') ' +
+				locations.rs2_map[map3_i][1],
+		});
+		markersArray.push(map3_marker);
+		google.maps.event.addListener(
+			map3_marker,
+			'click',
+			(function (map3_marker, map3_i) {
+				return function () {
+					var contentString =
+						'<div><b>(' +
+						locations.rs2_map[map3_i][0] +
+						') - ' +
+						locations.rs2_map[map3_i][1] +
+						'</b><hr style="margin-top: 5px; margin-bottom: 5px;">' +
+						locations.rs2_map[map3_i][5] +
+						'</div>';
+					map3_infowindow.setContent(contentString);
+					map3_infowindow.open(map3, map3_marker);
+					resetMarkerZIndex();
+					map3_marker.setZIndex(google.maps.Marker.MAX_ZINDEX + 1);
+				};
+			})(map3_marker, map3_i)
+		);
+	}
 }
 
 function exportMap(mapNum, mapType, imageType) {
-    // console.log("EXPORT MAP");
-    // display loading text when map is exporting
-    $('#ldpop-menu' + mapNum).html('Exporting Map <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span>');
-    $('#ldpop-menu' + mapNum).prop('disabled', true);
-    // use html2canvas js to convert google maps api div to canvas object
-    var map = $('#map' + mapNum).children().children()[0];
-    // console.log(map);
-    html2canvas(map, {
-        useCORS: true,
-        allowTaint: false,
-        async: true,
-        logging: false,
-        scale: 2
-    }).then(canvas => {
-        // convert canvas to image
-        var imgSRC = canvas.toDataURL("image/" + imageType);
-        // download image
-        var a = document.createElement('a');
-        a.setAttribute("type", "hidden");
-        a.href = imgSRC;
-        a.download = mapType + "-map." + imageType;
-        document.body.appendChild(a);
-        a.click();
-        document.body.removeChild(a);
-        // re-enable export dropdown after export is complete
-        $('#ldpop-menu' + mapNum).html('Export ' + mapType + ' Map <span class="caret"></span>');
-        $('#ldpop-menu' + mapNum).prop('disabled', false);
-    });
+	// console.log("EXPORT MAP");
+	// display loading text when map is exporting
+	$('#ldpop-menu' + mapNum).html(
+		'Exporting Map <i class="fa fa-spinner fa-pulse"></i><span class="sr-only">Loading</span>'
+	);
+	$('#ldpop-menu' + mapNum).prop('disabled', true);
+	// use html2canvas js to convert google maps api div to canvas object
+	var map = $('#map' + mapNum)
+		.children()
+		.children()[0];
+	// console.log(map);
+	html2canvas(map, {
+		useCORS: true,
+		allowTaint: false,
+		async: true,
+		logging: false,
+		scale: 2,
+	}).then((canvas) => {
+		// convert canvas to image
+		var imgSRC = canvas.toDataURL('image/' + imageType);
+		// download image
+		var a = document.createElement('a');
+		a.setAttribute('type', 'hidden');
+		a.href = imgSRC;
+		a.download = mapType + '-map.' + imageType;
+		document.body.appendChild(a);
+		a.click();
+		document.body.removeChild(a);
+		// re-enable export dropdown after export is complete
+		$('#ldpop-menu' + mapNum).html(
+			'Export ' + mapType + ' Map <span class="caret"></span>'
+		);
+		$('#ldpop-menu' + mapNum).prop('disabled', false);
+	});
 }
 
 function updateLDpop() {
-    var id = 'ldpop';
-    var $btn = $('#' + id).button('loading');
-    var population = getPopulationCodes(id+'-population-codes');
-    var r2_d;
-
-    if($('#pop_ld_r2').hasClass('active')) {
-        r2_d = 'r2'; // i.e. R2
-        $("#ldpop-ld-legend-img").attr('src', 'LDpop_legend_R2.png');
-    } else {
-        r2_d = 'd';  // i.e. Dprime
-        $("#ldpop-ld-legend-img").attr('src', 'LDpop_legend_Dprime.png');
-    }
-
-    var reference="ref" + Math.floor(Math.random() * (99999 - 10000 + 1))+ 10000;
-    var ldpopInputs = {
-        var1 : $('#ldpop-snp1').val(),
-        var2 : $('#ldpop-snp2').val(),
-        pop : population.join("+"),
-        genome_build: genomeBuild,
-        reference : reference,
-        r2_d: r2_d
-    };
-
-    updateHistoryURL(id, ldpopInputs);
-
-    var url = restServerUrl + "/ldpop";
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url,
-        data : ldpopInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        // console.log(data);
-        if (displayError(id, data) == false) {
-            $('#' + id + '-results-container').show();
-            console.log("LDpop data", data);
-            RefreshTable('#new-ldpop', data);
-            $("#ldpop_rs1").text(data.inputs.rs1 + " Allele Freq");
-            $("#ldpop_rs2").text(data.inputs.rs2 + " Allele Freq");
-            $(".ldpop-map1-title").html("<b>" + data.inputs.rs1 + " " + data.inputs.rs2 + " LD" + "</b>");
-            $(".ldpop-map2-title").html("<b>" + data.inputs.rs1 + " Allele Frequency" + "</b>");
-            $(".ldpop-map3-title").html("<b>" + data.inputs.rs2 + " Allele Frequency" + "</b>");
-            clearOverlays();
-            addMarkers(data);
-        }
-        $("#ldpop_results").text("Download Table");
-        $('#ldpop_results').css("text-decoration", "underline");
-        $("#ldpop_results").attr("href", "/LDlinkRestWeb/tmp/LDpop_"+reference+".txt");
-        $("#new-ldpop_filter").after($("#ldpop-download-table"));
-        if(!$('#new-ldpop_topInfo').length) {
-            $('<div id="new-ldpop_topInfo"></div>').prependTo('#new-ldpop_wrapper');
-        }    
-        $("#new-ldpop_topInfo").html($("#new-ldpop_info").clone().prop('id', 'new-ldpop_info_clone'));
-        $("#new-ldpop_info_clone").css("padding", "0px 10px 0px 0px");
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'ldpop';
+	var $btn = $('#' + id).button('loading');
+	var population = getPopulationCodes(id + '-population-codes');
+	var r2_d;
+
+	if ($('#pop_ld_r2').hasClass('active')) {
+		r2_d = 'r2'; // i.e. R2
+		$('#ldpop-ld-legend-img').attr('src', 'LDpop_legend_R2.png');
+	} else {
+		r2_d = 'd'; // i.e. Dprime
+		$('#ldpop-ld-legend-img').attr('src', 'LDpop_legend_Dprime.png');
+	}
+
+	var reference =
+		'ref' + Math.floor(Math.random() * (99999 - 10000 + 1)) + 10000;
+	var ldpopInputs = {
+		var1: $('#ldpop-snp1').val(),
+		var2: $('#ldpop-snp2').val(),
+		pop: population.join('+'),
+		genome_build: genomeBuild,
+		reference: reference,
+		r2_d: r2_d,
+	};
+
+	updateHistoryURL(id, ldpopInputs);
+
+	var url = restServerUrl + '/ldpop';
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: ldpopInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		// console.log(data);
+		if (displayError(id, data) == false) {
+			$('#' + id + '-results-container').show();
+			console.log('LDpop data', data);
+			RefreshTable('#new-ldpop', data);
+			$('#ldpop_rs1').text(data.inputs.rs1 + ' Allele Freq');
+			$('#ldpop_rs2').text(data.inputs.rs2 + ' Allele Freq');
+			$('.ldpop-map1-title').html(
+				'<b>' + data.inputs.rs1 + ' ' + data.inputs.rs2 + ' LD' + '</b>'
+			);
+			$('.ldpop-map2-title').html(
+				'<b>' + data.inputs.rs1 + ' Allele Frequency' + '</b>'
+			);
+			$('.ldpop-map3-title').html(
+				'<b>' + data.inputs.rs2 + ' Allele Frequency' + '</b>'
+			);
+			clearOverlays();
+			addMarkers(data);
+		}
+		$('#ldpop_results').text('Download Table');
+		$('#ldpop_results').css('text-decoration', 'underline');
+		$('#ldpop_results').attr(
+			'href',
+			'/LDlinkRestWeb/tmp/LDpop_' + reference + '.txt'
+		);
+		$('#new-ldpop_filter').after($('#ldpop-download-table'));
+		if (!$('#new-ldpop_topInfo').length) {
+			$('<div id="new-ldpop_topInfo"></div>').prependTo('#new-ldpop_wrapper');
+		}
+		$('#new-ldpop_topInfo').html(
+			$('#new-ldpop_info').clone().prop('id', 'new-ldpop_info_clone')
+		);
+		$('#new-ldpop_info_clone').css('padding', '0px 10px 0px 0px');
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function updateAPIaccess() {
-    var id = 'apiaccess';
-    var $btn = $('#' + id).button('loading');
-
-    var reference = "ref" + Math.floor(Math.random() * (99999 - 10000 + 1))+ 10000;
-    // if institution field was optional
-    // var institution_opt = $('#apiaccess-institution').val();
-    // if (institution_opt.length == 0) {
-    //     institution_opt = "NA"
-    // }
-
-    var apiaccessInputs = {
-        firstname: $('#apiaccess-firstname').val(),
-        lastname: $('#apiaccess-lastname').val(),
-        email: $('#apiaccess-email').val(),
-        institution: $('#apiaccess-institution').val(),
-        reference: reference
-    };
-
-    var url = restServerUrl + "/apiaccess/register_web";
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url,
-        data : apiaccessInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        $('.modal-title.apiaccess').empty().append(data.message);
-        $('.' + id + '-user-email').empty().append(data.email);
-        $('#apiblocked-firstname').val(data.firstname);
-        $('#apiblocked-lastname').val(data.lastname);
-        $('#apiblocked-institution').val(data.institution);
-        $('#apiblocked-email').val(data.email);
-        // $('#apiblocked-token').val(data.token);
-        $('#apiblocked-registered').val(data.registered);
-        $('#apiblocked-blocked').val(data.blocked);
-        if (data.message.substring(0, 5) == "Thank") {
-            // new user
-            $('#' + id + '-new-user').modal('show');
-        } else if (data.message.substring(0, 5) == "Email") { 
-            // existing user
-            $('#' + id + '-existing-user').modal('show');
-        } else {
-            // blocked user
-            $('#' + id + '-blocked-user').modal('show');
-        }
-        $('#' + id + '-loading').hide();
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'apiaccess';
+	var $btn = $('#' + id).button('loading');
+
+	var reference =
+		'ref' + Math.floor(Math.random() * (99999 - 10000 + 1)) + 10000;
+	// if institution field was optional
+	// var institution_opt = $('#apiaccess-institution').val();
+	// if (institution_opt.length == 0) {
+	//     institution_opt = "NA"
+	// }
+
+	var apiaccessInputs = {
+		firstname: $('#apiaccess-firstname').val(),
+		lastname: $('#apiaccess-lastname').val(),
+		email: $('#apiaccess-email').val(),
+		institution: $('#apiaccess-institution').val(),
+		reference: reference,
+	};
+
+	var url = restServerUrl + '/apiaccess/register_web';
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: apiaccessInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		$('.modal-title.apiaccess').empty().append(data.message);
+		$('.' + id + '-user-email')
+			.empty()
+			.append(data.email);
+		$('#apiblocked-firstname').val(data.firstname);
+		$('#apiblocked-lastname').val(data.lastname);
+		$('#apiblocked-institution').val(data.institution);
+		$('#apiblocked-email').val(data.email);
+		// $('#apiblocked-token').val(data.token);
+		$('#apiblocked-registered').val(data.registered);
+		$('#apiblocked-blocked').val(data.blocked);
+		if (data.message.substring(0, 5) == 'Thank') {
+			// new user
+			$('#' + id + '-new-user').modal('show');
+		} else if (data.message.substring(0, 5) == 'Email') {
+			// existing user
+			$('#' + id + '-existing-user').modal('show');
+		} else {
+			// blocked user
+			$('#' + id + '-blocked-user').modal('show');
+		}
+		$('#' + id + '-loading').hide();
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function updateAPIblocked() {
-    var id = 'apiblocked';
-    var $btn = $('#' + id).button('loading');
-
-    var reference = "ref" + Math.floor(Math.random() * (99999 - 10000 + 1))+ 10000;
-
-    var apiblockedInputs = {
-        firstname: $('#apiblocked-firstname').val(),
-        lastname: $('#apiblocked-lastname').val(),
-        institution: $('#apiblocked-institution').val(),
-        email: $('#apiblocked-email').val(),
-        // token: $('#apiblocked-token').val(),
-        registered: $('#apiblocked-registered').val(),
-        blocked: $('#apiblocked-blocked').val(),
-        justification: $('#apiblocked-justification').val(),
-        reference: reference
-    };
-
-    var url = restServerUrl + "/apiaccess/apiblocked_web";
-
-    var ajaxRequest = $.ajax({
-        type : "GET",
-        url : url,
-        data : apiblockedInputs,
-        contentType : 'application/json' // JSON
-    });
-
-    ajaxRequest.success(function(data) {
-        // reset form
-        $("#apiblocked-reset").click();
-        // hide loading animation
-        $('#' + id + '-loading').hide();
-        // hide form
-        $('#apiblocked-form').hide();
-        // hide submit button
-        $('#apiblocked').hide();
-        // show form submission message
-        $('#apiblocked-submit-message').show();
-        // change cancel to done button
-        $('#apiblocked-done').val("Done");
-    });
-    ajaxRequest.fail(function(jqXHR, textstatus) {
-        displayCommFail(id, jqXHR, textstatus);
-    });
-    ajaxRequest.always(function() {
-        $btn.button('reset');
-    });
-    hideLoadingIcon(ajaxRequest, id);
+	var id = 'apiblocked';
+	var $btn = $('#' + id).button('loading');
+
+	var reference =
+		'ref' + Math.floor(Math.random() * (99999 - 10000 + 1)) + 10000;
+
+	var apiblockedInputs = {
+		firstname: $('#apiblocked-firstname').val(),
+		lastname: $('#apiblocked-lastname').val(),
+		institution: $('#apiblocked-institution').val(),
+		email: $('#apiblocked-email').val(),
+		// token: $('#apiblocked-token').val(),
+		registered: $('#apiblocked-registered').val(),
+		blocked: $('#apiblocked-blocked').val(),
+		justification: $('#apiblocked-justification').val(),
+		reference: reference,
+	};
+
+	var url = restServerUrl + '/apiaccess/apiblocked_web';
+
+	var ajaxRequest = $.ajax({
+		type: 'GET',
+		url: url,
+		data: apiblockedInputs,
+		contentType: 'application/json', // JSON
+	});
+
+	ajaxRequest.success(function (data) {
+		// reset form
+		$('#apiblocked-reset').click();
+		// hide loading animation
+		$('#' + id + '-loading').hide();
+		// hide form
+		$('#apiblocked-form').hide();
+		// hide submit button
+		$('#apiblocked').hide();
+		// show form submission message
+		$('#apiblocked-submit-message').show();
+		// change cancel to done button
+		$('#apiblocked-done').val('Done');
+	});
+	ajaxRequest.fail(function (jqXHR, textstatus) {
+		displayCommFail(id, jqXHR, textstatus);
+	});
+	ajaxRequest.always(function () {
+		$btn.button('reset');
+	});
+	hideLoadingIcon(ajaxRequest, id);
 }
 
 function displayError(id, data) {
-    // Display error or warning if available.
-    var error = false;
-    if (data.traceback) {
-        console.warn("traceback");
-        console.warn(data.traceback);
-    }
-    if (data.warning) {
-        $('#' + id + '-message-warning').show();
-        $('#' + id + '-message-warning-content').empty().append(data.warning);
-        //hide error
-        $('#' + id + '-message').hide();
-    }
-
-    if (data.error) {
-        // ERROR
-        $('#' + id + '-message').show();
-        $('#' + id + '-message-content').empty().append(data.error);
-        //hide warning
-        $('#' + id + '-message-warning').hide();
-
-        //matrix specific
-        $('#'+id+"-download-links").hide();
-
-        $('#'+id+"-results-container").hide();
-
-        error = true;
-    }
-    return error;
+	// Display error or warning if available.
+	var error = false;
+	if (data.traceback) {
+		console.warn('traceback');
+		console.warn(data.traceback);
+	}
+	if (data.warning) {
+		$('#' + id + '-message-warning').show();
+		$('#' + id + '-message-warning-content')
+			.empty()
+			.append(data.warning);
+		//hide error
+		$('#' + id + '-message').hide();
+	}
+
+	if (data.error) {
+		// ERROR
+		$('#' + id + '-message').show();
+		$('#' + id + '-message-content')
+			.empty()
+			.append(data.error);
+		//hide warning
+		$('#' + id + '-message-warning').hide();
+
+		//matrix specific
+		$('#' + id + '-download-links').hide();
+
+		$('#' + id + '-results-container').hide();
+
+		error = true;
+	}
+	return error;
 }
 
 function displayCommFail(id, jqXHR, textstatus) {
-    //console.log(textstatus);
-    //console.dir(jqXHR);
-    console.warn("CommFail\n"+"status: "+textstatus+"\n"+jqXHR.statusText);
-    // var message = jqXHR.responseText;
-    // message += "<p>Internal Server Error: " + jqXHR.status + " - " + textstatus + "</p>";
-    // message = message.replace("[no address given]", "NCILDlinkWebAdmin@mail.nih.gov");
-   var message = "<p>Internal server error. Please contact LDlink admin.</p>"
-    if (jqXHR.status === 504){
-        message = "<p>The computation time is over 15 minutes. Server has no response.</p>"
-        message += "<p>Please split the input in multiple runs to avoid timeout"
-    }
-    $('#' + id + '-message').show();
-    $('#' + id + '-message-content').empty().append(message);
-    $('#' + id + '-progress').hide();
-    $('#' + id+ '-results-container').hide();
-    //hide loading icon
-    $('#'+id+"-loading").hide();
+	//console.log(textstatus);
+	//console.dir(jqXHR);
+	console.warn(
+		'CommFail\n' + 'status: ' + textstatus + '\n' + jqXHR.statusText
+	);
+	// var message = jqXHR.responseText;
+	// message += "<p>Internal Server Error: " + jqXHR.status + " - " + textstatus + "</p>";
+	// message = message.replace("[no address given]", "NCILDlinkWebAdmin@mail.nih.gov");
+	var message = '<p>Internal server error. Please contact LDlink admin.</p>';
+	if (jqXHR.status === 504) {
+		message =
+			'<p>The computation time is over 15 minutes. Server has no response.</p>';
+		message += '<p>Please split the input in multiple runs to avoid timeout';
+	}
+	$('#' + id + '-message').show();
+	$('#' + id + '-message-content')
+		.empty()
+		.append(message);
+	$('#' + id + '-progress').hide();
+	$('#' + id + '-results-container').hide();
+	//hide loading icon
+	$('#' + id + '-loading').hide();
 }
 
-
 // function displayCommFail(id, jqXHR, textstatus) {
 //     console.dir(jqXHR);
 //     console.warn("CommFail\n"+"status: "+textstatus);
@@ -4705,871 +5805,896 @@ function displayCommFail(id, jqXHR, textstatus) {
 //     //hide loading icon
 //     $('#'+id+"-loading").hide();
 
-    //
-    //  Display either a warning an error.
-    //
-    // $("#right_panel").show();
-    // $("#help").hide();
-    // $("#icon").css('visibility', 'visible');
-
-    // console.log("Show Message");
-
-    // var css_class = "";
-    // var header = "";
-    // var container_id = id+"-message-container";
-    // // console.log(container_id);
-
-    // if(message_type.toUpperCase() == 'ERROR') {
-    //     css_class = 'panel-danger';
-    //     header = 'Error';
-    // } else {
-    //     css_class = 'panel-warning';
-    //     header = 'Warning';
-    // }
-    // $("#"+container_id).empty().show();
-    // $("#"+container_id).append(
-    //     $('<div>')
-    //         .addClass('panel')
-    //         .addClass(css_class)
-    //         .append(
-    //             $('<div>')
-    //                 .addClass('panel-heading')
-    //                 .append(header)
-    //                 )
-    //         .append(
-    //             $('<div>')
-    //                 .addClass('panel-body')
-    //                 .append(message)
-    //                 )
-    //     );
+//
+//  Display either a warning an error.
+//
+// $("#right_panel").show();
+// $("#help").hide();
+// $("#icon").css('visibility', 'visible');
+
+// console.log("Show Message");
+
+// var css_class = "";
+// var header = "";
+// var container_id = id+"-message-container";
+// // console.log(container_id);
+
+// if(message_type.toUpperCase() == 'ERROR') {
+//     css_class = 'panel-danger';
+//     header = 'Error';
+// } else {
+//     css_class = 'panel-warning';
+//     header = 'Warning';
+// }
+// $("#"+container_id).empty().show();
+// $("#"+container_id).append(
+//     $('<div>')
+//         .addClass('panel')
+//         .addClass(css_class)
+//         .append(
+//             $('<div>')
+//                 .addClass('panel-heading')
+//                 .append(header)
+//                 )
+//         .append(
+//             $('<div>')
+//                 .addClass('panel-body')
+//                 .append(message)
+//                 )
+//     );
 // }
 
 function addLDHapHyperLinks(request, ldhapTable) {
-    $('#ldhap-snps').attr('href', '/LDlinkRestWeb/tmp/snps_' + request + '.txt');
-    $('#ldhap-haplotypes').attr('href', '/LDlinkRestWeb/tmp/haplotypes_' + request + '.txt');
-
-    var server;
-    var params = {};
-    var rs_number;
-    var url;
-    //server = 'http://genome.ucsc.edu/cgi-bin/hgTracks';
-    //console.log("ldhapData");
-
-
-    $.each(ldhapTable.rows, function(index, value) {
-        //console.log(index + ": " + value);
-        // Create RSnumber link (Cluster Report)
-        //server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
-        var server = 'http://www.ncbi.nlm.nih.gov/snp/';
-        // snp1-rsum
-        rs_number = value.RS.substring(2);
-        params = {
-            rs : rs_number
-        };
-        //url = server + "?" + $.param(params);
-        url = server  + value.RS;
-        $('#RSnumber_hap_' + index + ' a:first-child').attr('href', url);
-
-        // Create Coord link ()
-        server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
-        positions = value.Coord.split(":");
-        chr = positions[0];
-        mid_value = parseInt(positions[1]);
-        offset = 250;
-        range = (mid_value - offset) + "-" + (mid_value + offset);
-        position = chr + ":" + range;
-        rs_number = value.RS;
-        params = {
-            db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
-            position : position,
-            snp151 : 'pack',
-            'hgFind.matches' : rs_number
-        };
-        url = server + "?" + $.param(params);
-        //url = server  + value.RS;
-        $('#Coord_hap_' + index + ' a:first-child').attr('href', url);
-    });
-
+	$('#ldhap-snps').attr('href', '/LDlinkRestWeb/tmp/snps_' + request + '.txt');
+	$('#ldhap-haplotypes').attr(
+		'href',
+		'/LDlinkRestWeb/tmp/haplotypes_' + request + '.txt'
+	);
+
+	var server;
+	var params = {};
+	var rs_number;
+	var url;
+	//server = 'http://genome.ucsc.edu/cgi-bin/hgTracks';
+	//console.log("ldhapData");
+
+	$.each(ldhapTable.rows, function (index, value) {
+		//console.log(index + ": " + value);
+		// Create RSnumber link (Cluster Report)
+		//server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+		var server = 'http://www.ncbi.nlm.nih.gov/snp/';
+		// snp1-rsum
+		rs_number = value.RS.substring(2);
+		params = {
+			rs: rs_number,
+		};
+		//url = server + "?" + $.param(params);
+		url = server + value.RS;
+		$('#RSnumber_hap_' + index + ' a:first-child').attr('href', url);
+
+		// Create Coord link ()
+		server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
+		positions = value.Coord.split(':');
+		chr = positions[0];
+		mid_value = parseInt(positions[1]);
+		offset = 250;
+		range = mid_value - offset + '-' + (mid_value + offset);
+		position = chr + ':' + range;
+		rs_number = value.RS;
+		params = {
+			db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
+			position: position,
+			snp151: 'pack',
+			'hgFind.matches': rs_number,
+		};
+		url = server + '?' + $.param(params);
+		//url = server  + value.RS;
+		$('#Coord_hap_' + index + ' a:first-child').attr('href', url);
+	});
 }
 
 function addLDpairHyperLinks(data) {
-
-    // Add snp1-rsum to
-    var server;
-    var params = {};
-    var rs_number;
-    var url;
-    //
-    // Cluster Report:
-    //
-    //server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
-    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
-    //url = server + rs_number;
-    // snp1-rsum
-    rs_number = data.snp1.rsnum.substring(2);
-    //console.log(data)
-    params = {
-        rs : rs_number
-    };
-    //url = server + "?" + $.param(params);
-    url = server + rs_number;
-    $('#snp1-rsnum').attr('href', url)
-    // snp2-rsum
-    rs_number = data.snp2.rsnum.substring(2);
-    params = {
-        rs : rs_number
-    };
-    url = server + "?" + $.param(params);
-    $('#snp2-rsnum').attr('href', url)
-    //
-    // Genome Browser:
-    //
-    server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
-    // snp1-coord
-    var positions = data.snp1.coord.split(":");
-    var chr = positions[0];
-    var mid_value = parseInt(positions[1]);
-    var offset = 250;
-    var range = (mid_value - offset) + "-" + (mid_value + offset);
-    var position = chr + ":" + range;
-    rs_number = data.snp1.rsnum;
-    params = {
-        db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
-        position : position,
-        snp151 : 'pack',
-        'hgFind.matches' : rs_number
-    };
-    url = server + "?" + $.param(params);
-    $('#snp1-coord').attr('href', url)
-    // snp2-coord
-    positions = data.snp2.coord.split(":");
-    chr = positions[0];
-    mid_value = parseInt(positions[1]);
-    offset = 250;
-    range = (mid_value - offset) + "-" + (mid_value + offset);
-    position = chr + ":" + range;
-    rs_number = data.snp2.rsnum;
-    params = {
-        db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
-        position : position,
-        snp151 : 'pack',
-        'hgFind.matches' : rs_number
-    };
-    url = server + "?" + $.param(params);
-    $('#snp2-coord').attr('href', url);
-
+	// Add snp1-rsum to
+	var server;
+	var params = {};
+	var rs_number;
+	var url;
+	//
+	// Cluster Report:
+	//
+	//server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+	var server = 'http://www.ncbi.nlm.nih.gov/snp/';
+	//url = server + rs_number;
+	// snp1-rsum
+	rs_number = data.snp1.rsnum.substring(2);
+	//console.log(data)
+	params = {
+		rs: rs_number,
+	};
+	//url = server + "?" + $.param(params);
+	url = server + rs_number;
+	$('#snp1-rsnum').attr('href', url);
+	// snp2-rsum
+	rs_number = data.snp2.rsnum.substring(2);
+	params = {
+		rs: rs_number,
+	};
+	url = server + '?' + $.param(params);
+	$('#snp2-rsnum').attr('href', url);
+	//
+	// Genome Browser:
+	//
+	server = 'https://genome.ucsc.edu/cgi-bin/hgTracks';
+	// snp1-coord
+	var positions = data.snp1.coord.split(':');
+	var chr = positions[0];
+	var mid_value = parseInt(positions[1]);
+	var offset = 250;
+	var range = mid_value - offset + '-' + (mid_value + offset);
+	var position = chr + ':' + range;
+	rs_number = data.snp1.rsnum;
+	params = {
+		db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
+		position: position,
+		snp151: 'pack',
+		'hgFind.matches': rs_number,
+	};
+	url = server + '?' + $.param(params);
+	$('#snp1-coord').attr('href', url);
+	// snp2-coord
+	positions = data.snp2.coord.split(':');
+	chr = positions[0];
+	mid_value = parseInt(positions[1]);
+	offset = 250;
+	range = mid_value - offset + '-' + (mid_value + offset);
+	position = chr + ':' + range;
+	rs_number = data.snp2.rsnum;
+	params = {
+		db: genomeBuild == 'grch37' ? 'hg19' : 'hg38',
+		position: position,
+		snp151: 'pack',
+		'hgFind.matches': rs_number,
+	};
+	url = server + '?' + $.param(params);
+	$('#snp2-coord').attr('href', url);
 }
 
 function addCheckBox(code, description, elementId, platform_class) {
-    $("#"+elementId).append(
-        $("<div>").append(
-            $("<span>").addClass("platform-checkbox").append(
-                $("<input>").attr('type','checkbox')
-                    .attr('id',code)
-                    .attr('value', code)
-                    .prop('checked', true)
-                    .addClass(platform_class)
-                )
-            ).append(
-            $("<span>").addClass("formw").append(
-                $("<label>").attr('for',code)
-                    .css("font-weight", "normal")
-                    .text(description+" ("+code+")")
-                )
-        )
-    );
+	$('#' + elementId).append(
+		$('<div>')
+			.append(
+				$('<span>')
+					.addClass('platform-checkbox')
+					.append(
+						$('<input>')
+							.attr('type', 'checkbox')
+							.attr('id', code)
+							.attr('value', code)
+							.prop('checked', true)
+							.addClass(platform_class)
+					)
+			)
+			.append(
+				$('<span>')
+					.addClass('formw')
+					.append(
+						$('<label>')
+							.attr('for', code)
+							.css('font-weight', 'normal')
+							.text(description + ' (' + code + ')')
+					)
+			)
+	);
 }
 
 function buildPlatformSNPchip(data) {
-
-    //Change platforms to multiselect json
-
-    var platforms = JSON.parse(data);
-    var illumina = {};
-    var affymetrix = {};
-    snpchipReverseLookup =[];
-
-    $.each(platforms, function( code, description ) {
-        if(description.search("Affymetrix") >= 0) {
-            affymetrix[code] = description;
-            addCheckBox(code, description, "columnBcheckbox", "affymetrix");
-        }
-        if(description.search("Illumina") >= 0) {
-            illumina[code] = description;
-            addCheckBox(code, description, "columnAcheckbox", "illumina");
-        }
-        snpchipReverseLookup[description] = code;
-    });
-    $("#selectAllIllumina").prop('checked', true);
-    $("#selectAllAffymetrix").prop('checked', true);
-    calculateChipTotals();
+	//Change platforms to multiselect json
+
+	var platforms = JSON.parse(data);
+	var illumina = {};
+	var affymetrix = {};
+	snpchipReverseLookup = [];
+
+	$.each(platforms, function (code, description) {
+		if (description.search('Affymetrix') >= 0) {
+			affymetrix[code] = description;
+			addCheckBox(code, description, 'columnBcheckbox', 'affymetrix');
+		}
+		if (description.search('Illumina') >= 0) {
+			illumina[code] = description;
+			addCheckBox(code, description, 'columnAcheckbox', 'illumina');
+		}
+		snpchipReverseLookup[description] = code;
+	});
+	$('#selectAllIllumina').prop('checked', true);
+	$('#selectAllAffymetrix').prop('checked', true);
+	calculateChipTotals();
 }
 
 function buildTissueDropdown(elementId, tissueData) {
-    tissueJSON = JSON.parse(tissueData);
-    var htmlText = "";
-    if (tissueJSON.tissueInfo) {
-        var option = "<option value='TISSUE_VALUE'>TISSUE_NAME</option>\n";
-        for ( var tissue in tissueJSON.tissueInfo) {
-            var tissueObj = tissueJSON.tissueInfo[tissue];
-            if ("tissueSiteDetailId" in tissueObj && "tissueSiteDetail" in tissueObj){
-                htmlText += option
-                    .replace(/TISSUE_VALUE/g, tissueObj.tissueSiteDetailId)
-                    .replace(/TISSUE_NAME/g, tissueObj.tissueSiteDetail);
-            }
-        }
-    } else {
-        htmlText += "Error"
-    }
-
-    $('#' + elementId).html(htmlText);
-    //alert(elemtnId);
-    $('#' + elementId).multiselect({
-        enableClickableOptGroups : true,
-        buttonWidth : '180px',
-        maxHeight : 300,
-        buttonClass : 'btn btn-default btn-ldlink-multiselect',
-        includeSelectAllOption : true,
-        dropRight : false,
-        allSelectedText : 'All Tissues',
-        nonSelectedText : 'Select Tissue',
-        numberDisplayed : 1,
-        selectAllText : 'All Tissues',
-        previousOptionLength: 0,
-        // maxPopulationWarn: 2,
-        // maxPopulationWarnTimeout: 5000,
-        // maxPopulationWarnVisible: false,
-
-        // buttonClass: 'btn btn-link',
-        buttonText : function(options, select) {
-            // console.log("elementId: "+elementId);
-            // if(this.previousOptionLength < this.maxPopulationWarn && options.length >= this.maxPopulationWarn) {
-            //     $('#'+elementId+'-popover').popover('show');
-            //     this.maxPopulatinWarnVisible=true;
-            //     setTimeout(function(){
-            //         $('#'+elementId+'-popover').popover('destroy');
-            //         this.maxPopulatinWarnVisible=false;
-            //     }, this.maxPopulationWarnTimeout);
-            // } else {
-            //     //Destory popover if it is currently being displayed.
-            //     if(this.maxPopulatinWarnVisible) {
-            //         $('#'+elementId+'-popover').popover('destroy');
-            //     }
-            // }
-
-            if(options.length>0) {
-                $('#'+elementId+'-zero').popover('hide');
-            }
-            this.previousOptionLength = options.length;
-            if (options.length === 0) {
-                return this.nonSelectedText
-                        + '<span class="caret"></span>';
-            } else if (options.length == $('option', $(select)).length) {
-                return this.allSelectedText
-                        + '<span class="caret"></span>';
-            } else if (options.length > this.numberDisplayed) {
-                return '<span class="badge">' + options.length
-                        + '</span> ' + this.nSelectedText
-                        + '<span class="caret"></span>';
-            } else {
-                var selected = '';
-                options.each(function() {
-                    // var label = $(this).attr('label') :
-                    // $(this).html();
-                    var tissueText = $(this).text().length > 20 ? $(this).text().substring(0, 20) + "..." : $(this).text();
-                    selected += tissueText + '+';
-                });
-
-                return selected.substr(0, selected.length - 1)
-                        + ' <b class="caret"></b>';
-            }
-        },
-        buttonTitle : function(options, select) {
-            if (options.length === 0) {
-                return this.nonSelectedText;
-            } else {
-                var selected = '';
-                options.each(function() {
-                    selected += $(this).text() + '\n';
-                });
-                return selected;
-            }
-        },
-        onChange : function(option, checked) {
-            /*
+	tissueJSON = JSON.parse(tissueData);
+	var htmlText = '';
+	if (tissueJSON.tissueInfo) {
+		var option = "<option value='TISSUE_VALUE'>TISSUE_NAME</option>\n";
+		for (var tissue in tissueJSON.tissueInfo) {
+			var tissueObj = tissueJSON.tissueInfo[tissue];
+			if (
+				'tissueSiteDetailId' in tissueObj &&
+				'tissueSiteDetail' in tissueObj
+			) {
+				htmlText += option
+					.replace(/TISSUE_VALUE/g, tissueObj.tissueSiteDetailId)
+					.replace(/TISSUE_NAME/g, tissueObj.tissueSiteDetail);
+			}
+		}
+	} else {
+		htmlText += 'Error';
+	}
+
+	$('#' + elementId).html(htmlText);
+	//alert(elemtnId);
+	$('#' + elementId).multiselect({
+		enableClickableOptGroups: true,
+		buttonWidth: '180px',
+		maxHeight: 300,
+		buttonClass: 'btn btn-default btn-ldlink-multiselect',
+		includeSelectAllOption: true,
+		dropRight: false,
+		allSelectedText: 'All Tissues',
+		nonSelectedText: 'Select Tissue',
+		numberDisplayed: 1,
+		selectAllText: 'All Tissues',
+		previousOptionLength: 0,
+		// maxPopulationWarn: 2,
+		// maxPopulationWarnTimeout: 5000,
+		// maxPopulationWarnVisible: false,
+
+		// buttonClass: 'btn btn-link',
+		buttonText: function (options, select) {
+			// console.log("elementId: "+elementId);
+			// if(this.previousOptionLength < this.maxPopulationWarn && options.length >= this.maxPopulationWarn) {
+			//     $('#'+elementId+'-popover').popover('show');
+			//     this.maxPopulatinWarnVisible=true;
+			//     setTimeout(function(){
+			//         $('#'+elementId+'-popover').popover('destroy');
+			//         this.maxPopulatinWarnVisible=false;
+			//     }, this.maxPopulationWarnTimeout);
+			// } else {
+			//     //Destory popover if it is currently being displayed.
+			//     if(this.maxPopulatinWarnVisible) {
+			//         $('#'+elementId+'-popover').popover('destroy');
+			//     }
+			// }
+
+			if (options.length > 0) {
+				$('#' + elementId + '-zero').popover('hide');
+			}
+			this.previousOptionLength = options.length;
+			if (options.length === 0) {
+				return this.nonSelectedText + '<span class="caret"></span>';
+			} else if (options.length == $('option', $(select)).length) {
+				return this.allSelectedText + '<span class="caret"></span>';
+			} else if (options.length > this.numberDisplayed) {
+				return (
+					'<span class="badge">' +
+					options.length +
+					'</span> ' +
+					this.nSelectedText +
+					'<span class="caret"></span>'
+				);
+			} else {
+				var selected = '';
+				options.each(function () {
+					// var label = $(this).attr('label') :
+					// $(this).html();
+					var tissueText =
+						$(this).text().length > 20
+							? $(this).text().substring(0, 20) + '...'
+							: $(this).text();
+					selected += tissueText + '+';
+				});
+
+				return (
+					selected.substr(0, selected.length - 1) + ' <b class="caret"></b>'
+				);
+			}
+		},
+		buttonTitle: function (options, select) {
+			if (options.length === 0) {
+				return this.nonSelectedText;
+			} else {
+				var selected = '';
+				options.each(function () {
+					selected += $(this).text() + '\n';
+				});
+				return selected;
+			}
+		},
+		onChange: function (option, checked) {
+			/*
             var active_tab = $("#ldlink-tabs li:[class]='active']");
             console.dir(active_tab);
             */
-            //alert("You changed the population selection.");
-            //console.log("Option: ")
-            //console.dir(option[0]);
-            //console.log("checked: ")
-            //console.dir(checked);
-        }
-    });
-    if (!tissueJSON.tissueInfo) {
-        $('#' + elementId).multiselect("disable");
-    }
+			//alert("You changed the population selection.");
+			//console.log("Option: ")
+			//console.dir(option[0]);
+			//console.log("checked: ")
+			//console.dir(checked);
+		},
+	});
+	if (!tissueJSON.tissueInfo) {
+		$('#' + elementId).multiselect('disable');
+	}
 }
 
 function buildPopulationDropdown(elementId) {
-
-    var htmlText = "";
-    var htmlText1 = "<optgroup value='ABBREV' label='(ABBREV) FULLNAME'>\n";
-    var htmlText2 = "<option value='ABBREV'>(ABBREV) DETAIL </option>\n";
-    for ( var popAbbrev in populations) {
-        var population = populations[popAbbrev];
-        htmlText += htmlText1
-            .replace(/ABBREV/g, popAbbrev)
-            .replace("FULLNAME", population.fullName);
-        for ( var subPopAbbrev in population.subPopulations) {
-            var subDetail = population.subPopulations[subPopAbbrev];
-            htmlText += htmlText2
-                .replace(/ABBREV/g, subPopAbbrev).replace("DETAIL", subDetail);
-        }
-        htmlText += "</optgroup>\n";
-    }
-
-    $('#' + elementId).html(htmlText);
-    //alert(elemtnId);
-    $('#' + elementId).multiselect({
-        enableClickableOptGroups : true,
-        buttonWidth : '180px',
-        maxHeight : 400,
-        buttonClass : 'btn btn-default btn-ldlink-multiselect',
-        includeSelectAllOption : true,
-        dropRight : false,
-        allSelectedText : 'All Populations',
-        nonSelectedText : 'Select Population',
-        numberDisplayed : 4,
-        selectAllText : ' (ALL) All Populations',
-        previousOptionLength: 0,
-        maxPopulationWarn: 2,
-        maxPopulationWarnTimeout: 5000,
-        maxPopulationWarnVisible: false,
-
-        // buttonClass: 'btn btn-link',
-        buttonText : function(options, select) {
-            //console.log("elementId: "+elementId);
-            if(this.previousOptionLength < this.maxPopulationWarn && options.length >= this.maxPopulationWarn) {
-                $('#'+elementId+'-popover').popover('show');
-                this.maxPopulatinWarnVisible=true;
-                setTimeout(function(){
-                    $('#'+elementId+'-popover').popover('destroy');
-                    this.maxPopulatinWarnVisible=false;
-                }, this.maxPopulationWarnTimeout);
-            } else {
-                //Destory popover if it is currently being displayed.
-                if(this.maxPopulatinWarnVisible) {
-                    $('#'+elementId+'-popover').popover('destroy');
-                }
-            }
-
-            if(options.length>0) {
-                $('#'+elementId+'-zero').popover('hide');
-            }
-            this.previousOptionLength = options.length;
-            if (options.length === 0) {
-                return this.nonSelectedText
-                        + '<span class="caret"></span>';
-            } else if (options.length == $('option', $(select)).length) {
-                return this.allSelectedText
-                        + '<span class="caret"></span>';
-            } else if (options.length > this.numberDisplayed) {
-                return '<span class="badge">' + options.length
-                        + '</span> ' + this.nSelectedText
-                        + '<span class="caret"></span>';
-            } else {
-                var selected = '';
-                options.each(function() {
-                    // var label = $(this).attr('label') :
-                    // $(this).html();
-                    selected += $(this).val() + '+';
-                });
-
-                return selected.substr(0, selected.length - 1)
-                        + ' <b class="caret"></b>';
-            }
-        },
-        buttonTitle : function(options, select) {
-            if (options.length === 0) {
-                return this.nonSelectedText;
-            } else {
-                var selected = '';
-                options.each(function() {
-                    selected += $(this).text() + '\n';
-                });
-                return selected;
-            }
-        },
-        onChange : function(option, checked) {
-            /*
+	var htmlText = '';
+	var htmlText1 = "<optgroup value='ABBREV' label='(ABBREV) FULLNAME'>\n";
+	var htmlText2 = "<option value='ABBREV'>(ABBREV) DETAIL </option>\n";
+	for (var popAbbrev in populations) {
+		var population = populations[popAbbrev];
+		htmlText += htmlText1
+			.replace(/ABBREV/g, popAbbrev)
+			.replace('FULLNAME', population.fullName);
+		for (var subPopAbbrev in population.subPopulations) {
+			var subDetail = population.subPopulations[subPopAbbrev];
+			htmlText += htmlText2
+				.replace(/ABBREV/g, subPopAbbrev)
+				.replace('DETAIL', subDetail);
+		}
+		htmlText += '</optgroup>\n';
+	}
+
+	$('#' + elementId).html(htmlText);
+	//alert(elemtnId);
+	$('#' + elementId).multiselect({
+		enableClickableOptGroups: true,
+		buttonWidth: '180px',
+		maxHeight: 400,
+		buttonClass: 'btn btn-default btn-ldlink-multiselect',
+		includeSelectAllOption: true,
+		dropRight: false,
+		allSelectedText: 'All Populations',
+		nonSelectedText: 'Select Population',
+		numberDisplayed: 4,
+		selectAllText: ' (ALL) All Populations',
+		previousOptionLength: 0,
+		maxPopulationWarn: 2,
+		maxPopulationWarnTimeout: 5000,
+		maxPopulationWarnVisible: false,
+
+		// buttonClass: 'btn btn-link',
+		buttonText: function (options, select) {
+			//console.log("elementId: "+elementId);
+			if (
+				this.previousOptionLength < this.maxPopulationWarn &&
+				options.length >= this.maxPopulationWarn
+			) {
+				$('#' + elementId + '-popover').popover('show');
+				this.maxPopulatinWarnVisible = true;
+				setTimeout(function () {
+					$('#' + elementId + '-popover').popover('destroy');
+					this.maxPopulatinWarnVisible = false;
+				}, this.maxPopulationWarnTimeout);
+			} else {
+				//Destory popover if it is currently being displayed.
+				if (this.maxPopulatinWarnVisible) {
+					$('#' + elementId + '-popover').popover('destroy');
+				}
+			}
+
+			if (options.length > 0) {
+				$('#' + elementId + '-zero').popover('hide');
+			}
+			this.previousOptionLength = options.length;
+			if (options.length === 0) {
+				return this.nonSelectedText + '<span class="caret"></span>';
+			} else if (options.length == $('option', $(select)).length) {
+				return this.allSelectedText + '<span class="caret"></span>';
+			} else if (options.length > this.numberDisplayed) {
+				return (
+					'<span class="badge">' +
+					options.length +
+					'</span> ' +
+					this.nSelectedText +
+					'<span class="caret"></span>'
+				);
+			} else {
+				var selected = '';
+				options.each(function () {
+					// var label = $(this).attr('label') :
+					// $(this).html();
+					selected += $(this).val() + '+';
+				});
+
+				return (
+					selected.substr(0, selected.length - 1) + ' <b class="caret"></b>'
+				);
+			}
+		},
+		buttonTitle: function (options, select) {
+			if (options.length === 0) {
+				return this.nonSelectedText;
+			} else {
+				var selected = '';
+				options.each(function () {
+					selected += $(this).text() + '\n';
+				});
+				return selected;
+			}
+		},
+		onChange: function (option, checked) {
+			/*
             var active_tab = $("#ldlink-tabs li:[class]='active']");
             console.dir(active_tab);
             */
-            //alert("You changed the population selection.");
-            //console.log("Option: ")
-            //console.dir(option[0]);
-            //console.log("checked: ")
-            //console.dir(checked);
-        }
-    });
-
-    //console.log(elementId);
-    //console.dir($('#' + elementId));
-
+			//alert("You changed the population selection.");
+			//console.log("Option: ")
+			//console.dir(option[0]);
+			//console.log("checked: ")
+			//console.dir(checked);
+		},
+	});
 
+	//console.log(elementId);
+	//console.dir($('#' + elementId));
 }
 
 function getPopulationCodes(id) {
-    var population;
-    var totalPopulations;
-    population =  $('#'+id).val();
-    totalPopulations = countSubPopulations(populations);
-
-    //console.log("Populations (static)");
-    //console.log("Populations length: "+totalPopulations);
-
-    //console.dir(populations);
-    //console.log("Population selected");
-    //console.log("Population length: "+population.length);
-
-    //Check for selection of All
-    // If total subPopulations equals number of population then popluation = array("All");
-    if(totalPopulations == population.length) {
-        population = ["ALL"];
-        return population;
-    }
+	var population;
+	var totalPopulations;
+	population = $('#' + id).val();
+	totalPopulations = countSubPopulations(populations);
+
+	//console.log("Populations (static)");
+	//console.log("Populations length: "+totalPopulations);
+
+	//console.dir(populations);
+	//console.log("Population selected");
+	//console.log("Population length: "+population.length);
+
+	//Check for selection of All
+	// If total subPopulations equals number of population then popluation = array("All");
+	if (totalPopulations == population.length) {
+		population = ['ALL'];
+		return population;
+	}
 
-    population = replaceSubGroups(population);
+	population = replaceSubGroups(population);
 
-    return population;
+	return population;
 }
 
 function countSubPopulations(populations) {
+	var totalPopulations = 0;
+	var subPopulations;
 
-    var totalPopulations = 0;
-    var subPopulations;
+	$.each(populations, function (i, val) {
+		totalPopulations += Number(Object.size(val.subPopulations));
+	});
 
-    $.each(populations, function(i, val) {
-        totalPopulations += Number(Object.size(val.subPopulations));
-    });
-
-    return totalPopulations;
+	return totalPopulations;
 }
 
 function replaceSubGroups(population) {
-    var totalGroupPopulations = 0;
-    var subPopulationsFound = 0;
-    var currentSubPopulations = [];
-    //Determine if a group has all subPopulations selected.
-    $.each(populations, function(currentGroup, val) {
-        totalGroupPopulations = Number(Object.size(val.subPopulations));
-        subPopulationsFound = 0;
-        currentSubPopulations = [];
-        //if there is one miss then abbondon effort
-        $.each(val.subPopulations, function(pop, desc) {
-            if($.inArray(pop, population) !== -1) {
-                subPopulationsFound++;
-                currentSubPopulations.push(pop);
-                //console.log("pop found: "+pop);
-            } else {
-                missingPop = true;
-                //console.log("pop missing: "+pop);
-            }
-        });
-        if(currentSubPopulations.length == totalGroupPopulations) {
-            //Remove populations of Group then add Group acronymn
-            $.each(currentSubPopulations, function(key, value) {
-                //Find position in array
-                population.splice( $.inArray(value, population), 1 );
-            });
-            population.push(currentGroup);
-
-        }
-        //If all are found then
-        //totalPopulations += Number(Object.size(val.subPopulations));
-    });
-
-    return population;
+	var totalGroupPopulations = 0;
+	var subPopulationsFound = 0;
+	var currentSubPopulations = [];
+	//Determine if a group has all subPopulations selected.
+	$.each(populations, function (currentGroup, val) {
+		totalGroupPopulations = Number(Object.size(val.subPopulations));
+		subPopulationsFound = 0;
+		currentSubPopulations = [];
+		//if there is one miss then abbondon effort
+		$.each(val.subPopulations, function (pop, desc) {
+			if ($.inArray(pop, population) !== -1) {
+				subPopulationsFound++;
+				currentSubPopulations.push(pop);
+				//console.log("pop found: "+pop);
+			} else {
+				missingPop = true;
+				//console.log("pop missing: "+pop);
+			}
+		});
+		if (currentSubPopulations.length == totalGroupPopulations) {
+			//Remove populations of Group then add Group acronymn
+			$.each(currentSubPopulations, function (key, value) {
+				//Find position in array
+				population.splice($.inArray(value, population), 1);
+			});
+			population.push(currentGroup);
+		}
+		//If all are found then
+		//totalPopulations += Number(Object.size(val.subPopulations));
+	});
+
+	return population;
 }
 
 function addValidators() {
-     $('#snpclipForm').formValidation({
-        framework: 'bootstrap',
-        icon: {
-            valid: 'glyphicon glyphicon-ok',
-            invalid: 'glyphicon glyphicon-remove',
-            validating: 'glyphicon glyphicon-refresh'
-        },
-        fields: {
-            price: {
-                validators: {
-                    notEmpty: {
-                        message: 'The price is required'
-                    },
-                    numeric: {
-                        message: 'The price must be a number'
-                    }
-                }
-            },
-            amount: {
-                validators: {
-                    notEmpty: {
-                        message: 'The amount is required'
-                    },
-                    numeric: {
-                        message: 'The amount must be a number'
-                    }
-                }
-            },
-            color: {
-                validators: {
-                    notEmpty: {
-                        message: 'The color is required'
-                    }
-                }
-            },
-            size: {
-                validators: {
-                    notEmpty: {
-                        message: 'The size is required'
-                    }
-                }
-            }
-        }
-    });
-
+	$('#snpclipForm').formValidation({
+		framework: 'bootstrap',
+		icon: {
+			valid: 'glyphicon glyphicon-ok',
+			invalid: 'glyphicon glyphicon-remove',
+			validating: 'glyphicon glyphicon-refresh',
+		},
+		fields: {
+			price: {
+				validators: {
+					notEmpty: {
+						message: 'The price is required',
+					},
+					numeric: {
+						message: 'The price must be a number',
+					},
+				},
+			},
+			amount: {
+				validators: {
+					notEmpty: {
+						message: 'The amount is required',
+					},
+					numeric: {
+						message: 'The amount must be a number',
+					},
+				},
+			},
+			color: {
+				validators: {
+					notEmpty: {
+						message: 'The color is required',
+					},
+				},
+			},
+			size: {
+				validators: {
+					notEmpty: {
+						message: 'The size is required',
+					},
+				},
+			},
+		},
+	});
 }
 
 /* Utilities */
 
-$(document).ready(function() {
-    $('#ldhap-file-snp-numbers').keyup(validateTextarea);
-    $('#ldmatrix-file-snp-numbers').keyup(validateTextarea);
-    $('#ldexpress-file-snp-numbers').keyup(validateTextarea);
-    $('#ldexpress-bp-window').keyup(validateLDexpressBasePairWindow);
-    $('#ldtrait-file-snp-numbers').keyup(validateTextarea);
-    $('#ldproxy-bp-window').keyup(validateLDproxyBasePairWindow);
-    $('#ldtrait-bp-window').keyup(validateLDtraitBasePairWindow);
-    $('#snpchip-file-snp-numbers').keyup(validateTextarea);
-    $('#snpclip-file-snp-numbers').keyup(validateTextarea);
-    $('#region-gene-base-pair-window').keyup(validateBasePairWindows);
-    $('#region-variant-base-pair-window').keyup(validateBasePairWindows);
-    $('#region-variant-index').keyup(validateIndex);
-    $('#region-region-start-coord').keyup(validateChr);
-    $('#region-region-end-coord').keyup(validateChr);
-    $('#region-region-index').keyup(validateIndex);
-    $('#region-gene-index').keyup(validateIndex);
-    $('#region-gene-name').keyup(validateGeneName);
-
+$(document).ready(function () {
+	$('#ldhap-file-snp-numbers').keyup(validateTextarea);
+	$('#ldmatrix-file-snp-numbers').keyup(validateTextarea);
+	$('#ldexpress-file-snp-numbers').keyup(validateTextarea);
+	$('#ldexpress-bp-window').keyup(validateLDexpressBasePairWindow);
+	$('#ldtrait-file-snp-numbers').keyup(validateTextarea);
+	$('#ldproxy-bp-window').keyup(validateLDproxyBasePairWindow);
+	$('#ldtrait-bp-window').keyup(validateLDtraitBasePairWindow);
+	$('#snpchip-file-snp-numbers').keyup(validateTextarea);
+	$('#snpclip-file-snp-numbers').keyup(validateTextarea);
+	$('#region-gene-base-pair-window').keyup(validateBasePairWindows);
+	$('#region-variant-base-pair-window').keyup(validateBasePairWindows);
+	$('#region-variant-index').keyup(validateIndex);
+	$('#region-region-start-coord').keyup(validateChr);
+	$('#region-region-end-coord').keyup(validateChr);
+	$('#region-region-index').keyup(validateIndex);
+	$('#region-gene-index').keyup(validateIndex);
+	$('#region-gene-name').keyup(validateGeneName);
 });
 
 function validateGeneName() {
-    var errorMsg = "Enter a valid Gene Name";
-    var textarea = this;
-    // console.log($(textarea).attr('pattern'));
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', "i");
-    //Check to see if user selected chr10 thru chr22.
-    var currentValue = $(this).val();
-    $(this).val(currentValue.toUpperCase());
-    var hasError = !currentValue.match(pattern);
-    // console.log('hasError:'+hasError);
-    $(textarea).toggleClass('error', !!hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-    } else {
-        $(textarea).removeAttr('title');
-    }
+	var errorMsg = 'Enter a valid Gene Name';
+	var textarea = this;
+	// console.log($(textarea).attr('pattern'));
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', 'i');
+	//Check to see if user selected chr10 thru chr22.
+	var currentValue = $(this).val();
+	$(this).val(currentValue.toUpperCase());
+	var hasError = !currentValue.match(pattern);
+	// console.log('hasError:'+hasError);
+	$(textarea).toggleClass('error', !!hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+	} else {
+		$(textarea).removeAttr('title');
+	}
 }
 
 function validateChr() {
-    var errorMsg = "chr(1-22 or X or Y):######";
-    var textarea = this;
-    // console.log($(textarea).attr('pattern'));
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', "i");
-    var currentValue = $(this).val();
-    var hasError = !currentValue.match(pattern);
-    // console.log('hasError:'+hasError);
-    $(textarea).toggleClass('error', !!hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    //textarea.setCustomValidity('Hello');
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-    } else {
-        $(textarea).removeAttr('title');
-    }
+	var errorMsg = 'chr(1-22 or X or Y):######';
+	var textarea = this;
+	// console.log($(textarea).attr('pattern'));
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', 'i');
+	var currentValue = $(this).val();
+	var hasError = !currentValue.match(pattern);
+	// console.log('hasError:'+hasError);
+	$(textarea).toggleClass('error', !!hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	//textarea.setCustomValidity('Hello');
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+	} else {
+		$(textarea).removeAttr('title');
+	}
 }
 
 function validateIndex() {
-    var errorMsg = "chr(1-22 or X or Y):###### or rs######";
-    var textarea = this;
-    // console.log($(textarea).attr('pattern'));
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', "i");
-    var currentValue = $(this).val();
-    var hasError = !currentValue.match(pattern);
-    // console.log('hasError:'+hasError);
-    $(textarea).toggleClass('error', !!hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    //textarea.setCustomValidity('Hello');
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-    } else {
-        $(textarea).removeAttr('title');
-    }
+	var errorMsg = 'chr(1-22 or X or Y):###### or rs######';
+	var textarea = this;
+	// console.log($(textarea).attr('pattern'));
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$', 'i');
+	var currentValue = $(this).val();
+	var hasError = !currentValue.match(pattern);
+	// console.log('hasError:'+hasError);
+	$(textarea).toggleClass('error', !!hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	//textarea.setCustomValidity('Hello');
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+	} else {
+		$(textarea).removeAttr('title');
+	}
 }
 
 function validateLDexpressBasePairWindow() {
-    var errorMsg = "Value must be a number between 0 and 1,000,000";
-    var textarea = "#ldexpress-bp-window";
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
-    var currentValue = $(textarea).val();
-    var currentValueNoCommas = currentValue.replace(/\,/g, '');
-    var hasError = !currentValue.match(pattern) || (currentValueNoCommas < 0 || currentValueNoCommas > 1000000);
-    $(textarea).toggleClass('error', hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-        return false;
-    } else {
-        return true;
-    }
+	var errorMsg = 'Value must be a number between 0 and 1,000,000';
+	var textarea = '#ldexpress-bp-window';
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
+	var currentValue = $(textarea).val();
+	var currentValueNoCommas = currentValue.replace(/\,/g, '');
+	var hasError =
+		!currentValue.match(pattern) ||
+		currentValueNoCommas < 0 ||
+		currentValueNoCommas > 1000000;
+	$(textarea).toggleClass('error', hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+		return false;
+	} else {
+		return true;
+	}
 }
 
 function validateLDproxyBasePairWindow() {
-    var errorMsg = "Value must be a number between 0 and 1,000,000";
-    var textarea = "#ldproxy-bp-window";
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
-    var currentValue = $(textarea).val();
-    var currentValueNoCommas = currentValue.replace(/\,/g, '');
-    var hasError = !currentValue.match(pattern) || (currentValueNoCommas < 0 || currentValueNoCommas > 1000000);
-    $(textarea).toggleClass('error', hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-        return false;
-    } else {
-        return true;
-    }
+	var errorMsg = 'Value must be a number between 0 and 1,000,000';
+	var textarea = '#ldproxy-bp-window';
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
+	var currentValue = $(textarea).val();
+	var currentValueNoCommas = currentValue.replace(/\,/g, '');
+	var hasError =
+		!currentValue.match(pattern) ||
+		currentValueNoCommas < 0 ||
+		currentValueNoCommas > 1000000;
+	$(textarea).toggleClass('error', hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+		return false;
+	} else {
+		return true;
+	}
 }
 
 function validateLDtraitBasePairWindow() {
-    var errorMsg = "Value must be a number between 0 and 1,000,000";
-    var textarea = "#ldtrait-bp-window";
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
-    var currentValue = $(textarea).val();
-    var currentValueNoCommas = currentValue.replace(/\,/g, '');
-    var hasError = !currentValue.match(pattern) || (currentValueNoCommas < 0 || currentValueNoCommas > 1000000);
-    $(textarea).toggleClass('error', hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-        return false;
-    } else {
-        return true;
-    }
+	var errorMsg = 'Value must be a number between 0 and 1,000,000';
+	var textarea = '#ldtrait-bp-window';
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
+	var currentValue = $(textarea).val();
+	var currentValueNoCommas = currentValue.replace(/\,/g, '');
+	var hasError =
+		!currentValue.match(pattern) ||
+		currentValueNoCommas < 0 ||
+		currentValueNoCommas > 1000000;
+	$(textarea).toggleClass('error', hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+		return false;
+	} else {
+		return true;
+	}
 }
 
 function validateBasePairWindows() {
-    var errorMsg = "Enter a positive number";
-    var textarea = this;
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
-    var currentValue = $(this).val();
-    var hasError = !currentValue.match(pattern);
-    // console.log('hasError:'+hasError);
-    $(textarea).toggleClass('error', !!hasError);
-    $(textarea).toggleClass('ok', !hasError);
-    if (hasError) {
-        $(textarea).attr('title', errorMsg);
-    } else {
-        $(textarea).removeAttr('title');
-    }
+	var errorMsg = 'Enter a positive number';
+	var textarea = this;
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
+	var currentValue = $(this).val();
+	var hasError = !currentValue.match(pattern);
+	// console.log('hasError:'+hasError);
+	$(textarea).toggleClass('error', !!hasError);
+	$(textarea).toggleClass('ok', !hasError);
+	if (hasError) {
+		$(textarea).attr('title', errorMsg);
+	} else {
+		$(textarea).removeAttr('title');
+	}
 }
 
 function validateTextarea() {
-    var errorMsg = "Please match the format requested: rs followed by 1 or more digits (ex: rs12345), no spaces permitted - or - chr(0-22, X, Y):##### (ex: chr1:12345)";
-    var textarea = this;
-    var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
-    // check each line of text
-    $.each($(this).val().split("\n"), function (index, value) {
-        // check if the line matches the patterns
-        //console.log(value);
-        var hasError = !this.match(pattern);
-        if(value == "" || value == "\n" || this.length<=2 )
-            hasError = false;
-        //console.log("hasError: "+hasError);
-        if (typeof textarea.setCustomValidity === 'function') {
-            textarea.setCustomValidity(hasError ? errorMsg : '');
-        } else {
-            // Not supported by the browser, fallback to manual error display...
-            $(textarea).toggleClass('error', !!hasError);
-            $(textarea).toggleClass('ok', !hasError);
-            if (hasError) {
-                $(textarea).attr('title', errorMsg);
-            } else {
-                $(textarea).removeAttr('title');
-            }
-        }
-        return !hasError;
-    });
+	var errorMsg =
+		'Please match the format requested: rs followed by 1 or more digits (ex: rs12345), no spaces permitted - or - chr(0-22, X, Y):##### (ex: chr1:12345)';
+	var textarea = this;
+	var pattern = new RegExp('^' + $(textarea).attr('pattern') + '$');
+	// check each line of text
+	$.each($(this).val().split('\n'), function (index, value) {
+		// check if the line matches the patterns
+		//console.log(value);
+		var hasError = !this.match(pattern);
+		if (value == '' || value == '\n' || this.length <= 2) hasError = false;
+		//console.log("hasError: "+hasError);
+		if (typeof textarea.setCustomValidity === 'function') {
+			textarea.setCustomValidity(hasError ? errorMsg : '');
+		} else {
+			// Not supported by the browser, fallback to manual error display...
+			$(textarea).toggleClass('error', !!hasError);
+			$(textarea).toggleClass('ok', !hasError);
+			if (hasError) {
+				$(textarea).attr('title', errorMsg);
+			} else {
+				$(textarea).removeAttr('title');
+			}
+		}
+		return !hasError;
+	});
 }
 
 function toggleChevron(e) {
-    $(e.target).prev('.panel-heading').find("i.indicator")
-        .toggleClass('glyphicon-chevron-down glyphicon-chevron-up');
+	$(e.target)
+		.prev('.panel-heading')
+		.find('i.indicator')
+		.toggleClass('glyphicon-chevron-down glyphicon-chevron-up');
 }
 
-Array.prototype.contains = function(v) {
-    for(var i = 0; i < this.length; i++) {
-        if(this[i] === v) return true;
-    }
-    return false;
+Array.prototype.contains = function (v) {
+	for (var i = 0; i < this.length; i++) {
+		if (this[i] === v) return true;
+	}
+	return false;
 };
 
-Array.prototype.unique = function() {
-    var arr = [];
-    for(var i = 0; i < this.length; i++) {
-        if(!arr.contains(this[i])) {
-            arr.push(this[i]);
-        }
-    }
-    return arr;
-}
+Array.prototype.unique = function () {
+	var arr = [];
+	for (var i = 0; i < this.length; i++) {
+		if (!arr.contains(this[i])) {
+			arr.push(this[i]);
+		}
+	}
+	return arr;
+};
 
 function parseFile(file, callback) {
-    var fileSize   = file.size;
-    var chunkSize  = 4 * 1024; // bytes
-    var offset     = 0;
-    var self       = this; // we need a reference to the current object
-    var chunkReaderBlock = null;
-
-    var readEventHandler = function(evt) {
-        if (evt.target.error == null) {
-            offset += evt.target.result.length;
-            callback(evt.target.result); // callback for handling read chunk
-            return; //Only call the callback once. return.
-        } else {
-            // console.log("Read error: " + evt.target.error);
-            return;
-        }
-        if (offset >= fileSize) {
-            // console.log("Done reading file");
-            return;
-        }
-        // of to the next chunk
-        chunkReaderBlock(offset, chunkSize, file);
-    }
-
-    chunkReaderBlock = function(_offset, length, _file) {
-        //console.log("Reading a block, offset is "+_offset);
-        var r = new FileReader();
-        var blob = _file.slice(_offset, length + _offset);
-        r.onload = readEventHandler;
-        r.readAsText(blob);
-    }
-
-    // now let's start the read with the first block
-    chunkReaderBlock(offset, chunkSize, file);
+	var fileSize = file.size;
+	var chunkSize = 4 * 1024; // bytes
+	var offset = 0;
+	var self = this; // we need a reference to the current object
+	var chunkReaderBlock = null;
+
+	var readEventHandler = function (evt) {
+		if (evt.target.error == null) {
+			offset += evt.target.result.length;
+			callback(evt.target.result); // callback for handling read chunk
+			return; //Only call the callback once. return.
+		} else {
+			// console.log("Read error: " + evt.target.error);
+			return;
+		}
+		if (offset >= fileSize) {
+			// console.log("Done reading file");
+			return;
+		}
+		// of to the next chunk
+		chunkReaderBlock(offset, chunkSize, file);
+	};
+
+	chunkReaderBlock = function (_offset, length, _file) {
+		//console.log("Reading a block, offset is "+_offset);
+		var r = new FileReader();
+		var blob = _file.slice(_offset, length + _offset);
+		r.onload = readEventHandler;
+		r.readAsText(blob);
+	};
+
+	// now let's start the read with the first block
+	chunkReaderBlock(offset, chunkSize, file);
 }
 
 function supportAjaxUploadWithProgress() {
-  return supportFileAPI() && supportAjaxUploadProgressEvents() && supportFormData();
+	return (
+		supportFileAPI() && supportAjaxUploadProgressEvents() && supportFormData()
+	);
 
-  function supportFileAPI() {
-    var fi = document.createElement('INPUT');
-    fi.type = 'file';
-    return 'files' in fi;
-  };
+	function supportFileAPI() {
+		var fi = document.createElement('INPUT');
+		fi.type = 'file';
+		return 'files' in fi;
+	}
 
-  function supportAjaxUploadProgressEvents() {
-    var xhr = new XMLHttpRequest();
-    return !! (xhr && ('upload' in xhr) && ('onprogress' in xhr.upload));
-  };
+	function supportAjaxUploadProgressEvents() {
+		var xhr = new XMLHttpRequest();
+		return !!(xhr && 'upload' in xhr && 'onprogress' in xhr.upload);
+	}
 
-  function supportFormData() {
-    return !! window.FormData;
-  }
+	function supportFormData() {
+		return !!window.FormData;
+	}
 }
 
-function createCookie(name,value,days) {
-    if (days) {
-        var date = new Date();
-        date.setTime(date.getTime()+(days*24*60*60*1000));
-        var expires = "; expires="+date.toGMTString();
-    }
-    else var expires = "";
-    document.cookie = name+"="+value+expires+"; path=/";
+function createCookie(name, value, days) {
+	if (days) {
+		var date = new Date();
+		date.setTime(date.getTime() + days * 24 * 60 * 60 * 1000);
+		var expires = '; expires=' + date.toGMTString();
+	} else var expires = '';
+	document.cookie = name + '=' + value + expires + '; path=/';
 }
 
 function readCookie(name) {
-    var nameEQ = name + "=";
-    var ca = document.cookie.split(';');
-    for(var i=0;i < ca.length;i++) {
-        var c = ca[i];
-        while (c.charAt(0)==' ') c = c.substring(1,c.length);
-        if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length,c.length);
-    }
-    return null;
+	var nameEQ = name + '=';
+	var ca = document.cookie.split(';');
+	for (var i = 0; i < ca.length; i++) {
+		var c = ca[i];
+		while (c.charAt(0) == ' ') c = c.substring(1, c.length);
+		if (c.indexOf(nameEQ) == 0) return c.substring(nameEQ.length, c.length);
+	}
+	return null;
 }
 
 function eraseCookie(name) {
-    createCookie(name,"",-1);
-}
-
-$("#news-right-arrow").on('click',  function() {
-    if($("#news-right-arrow").hasClass("enabled-news-scroller")){
-        console.log(homeStartBox)
-        if($('#news-card-outside-2').css("display") != "none"){
-            homeStartBox += 1;
-            $("#news-card-1").html(newsList[homeStartBox]);
-            $("#news-card-2").html(newsList[homeStartBox+1]);
-            $("#news-card-3").html(newsList[homeStartBox+2]);
-            if(homeStartBox + 3 >= newsList.length){
-                $("#news-right-arrow").removeClass("enabled-news-scroller")
-                $("#news-right-arrow").addClass("disabled-news-scroller")
-            }
-            if($("#news-left-arrow").hasClass("disabled-news-scroller")){
-                $("#news-left-arrow").addClass("enabled-news-scroller")
-                $("#news-left-arrow").removeClass("disabled-news-scroller")
-            }
-        }
-        else{
-            console.log(newsList)
-            if(homeStartBox < newsList.length-1){
-                homeStartBox += 1;
-                $("#news-card-1").html(newsList[homeStartBox]);
-                if(homeStartBox >= newsList.length - 1){
-                    $("#news-right-arrow").removeClass("enabled-news-scroller")
-                    $("#news-right-arrow").addClass("disabled-news-scroller")
-                }
-                if($("#news-left-arrow").hasClass("disabled-news-scroller")){
-                    $("#news-left-arrow").addClass("enabled-news-scroller")
-                    $("#news-left-arrow").removeClass("disabled-news-scroller")
-                }
-            }
-        }
-    }
+	createCookie(name, '', -1);
+}
+
+$('#news-right-arrow').on('click', function () {
+	if ($('#news-right-arrow').hasClass('enabled-news-scroller')) {
+		console.log(homeStartBox);
+		if ($('#news-card-outside-2').css('display') != 'none') {
+			homeStartBox += 1;
+			$('#news-card-1').html(newsList[homeStartBox]);
+			$('#news-card-2').html(newsList[homeStartBox + 1]);
+			$('#news-card-3').html(newsList[homeStartBox + 2]);
+			if (homeStartBox + 3 >= newsList.length) {
+				$('#news-right-arrow').removeClass('enabled-news-scroller');
+				$('#news-right-arrow').addClass('disabled-news-scroller');
+			}
+			if ($('#news-left-arrow').hasClass('disabled-news-scroller')) {
+				$('#news-left-arrow').addClass('enabled-news-scroller');
+				$('#news-left-arrow').removeClass('disabled-news-scroller');
+			}
+		} else {
+			console.log(newsList);
+			if (homeStartBox < newsList.length - 1) {
+				homeStartBox += 1;
+				$('#news-card-1').html(newsList[homeStartBox]);
+				if (homeStartBox >= newsList.length - 1) {
+					$('#news-right-arrow').removeClass('enabled-news-scroller');
+					$('#news-right-arrow').addClass('disabled-news-scroller');
+				}
+				if ($('#news-left-arrow').hasClass('disabled-news-scroller')) {
+					$('#news-left-arrow').addClass('enabled-news-scroller');
+					$('#news-left-arrow').removeClass('disabled-news-scroller');
+				}
+			}
+		}
+	}
 });
 
-$("#news-left-arrow").on('click',  function() {
-    if($("#news-left-arrow").hasClass("enabled-news-scroller")){
-        homeStartBox -= 1;
-        $("#news-card-1").html(newsList[homeStartBox]);
-        $("#news-card-2").html(newsList[homeStartBox+1]);
-        $("#news-card-3").html(newsList[homeStartBox+2]);
-        if(homeStartBox <= 0){
-            $("#news-left-arrow").removeClass("enabled-news-scroller")
-            $("#news-left-arrow").addClass("disabled-news-scroller")
-        }
-        if($("#news-right-arrow").hasClass("disabled-news-scroller")){
-            $("#news-right-arrow").addClass("enabled-news-scroller")
-            $("#news-right-arrow").removeClass("disabled-news-scroller")
-        }
-    }
+$('#news-left-arrow').on('click', function () {
+	if ($('#news-left-arrow').hasClass('enabled-news-scroller')) {
+		homeStartBox -= 1;
+		$('#news-card-1').html(newsList[homeStartBox]);
+		$('#news-card-2').html(newsList[homeStartBox + 1]);
+		$('#news-card-3').html(newsList[homeStartBox + 2]);
+		if (homeStartBox <= 0) {
+			$('#news-left-arrow').removeClass('enabled-news-scroller');
+			$('#news-left-arrow').addClass('disabled-news-scroller');
+		}
+		if ($('#news-right-arrow').hasClass('disabled-news-scroller')) {
+			$('#news-right-arrow').addClass('enabled-news-scroller');
+			$('#news-right-arrow').removeClass('disabled-news-scroller');
+		}
+	}
 });
 
-
 /*
 $(".dropdown-nav").on('click mouseover', function() {
     if($(".dropdown-nav .dropdown-content").css("display") == "block"){
@@ -5602,128 +6727,131 @@ $('.dropdown-toggle').click(function(e) {
     }
   });*/
 
-function testResize(){
-    // console.log("resized");
-    //if became smalle
-    if($('#news-card-outside-2').css('display') == "none"){
-        console.log("1 box")
-        if(homeStartBox < newsList.length - 1){
-            // console.log("does not exxist")
-            if($("#news-right-arrow").hasClass("disabled-news-scroller")){
-                $("#news-right-arrow").addClass("enabled-news-scroller")
-                $("#news-right-arrow").removeClass("disabled-news-scroller")
-            }
-        }
-    }
-    else if($('#news-card-outside-3').css('display') == 'none' && $('#news-card-outside-2').css('display') != 'none'){
-        
-        // console.log("2 boxes")
-        if(homeStartBox > newsList.length - 2){
-            homeStartBox = newsList.length - 2;
-        }
-        if($("#news-right-arrow").hasClass("disabled-news-scroller")){
-            $("#news-right-arrow").addClass("enabled-news-scroller")
-            $("#news-right-arrow").removeClass("disabled-news-scroller")
-        }
-        $("#news-card-1").html(newsList[homeStartBox]);
-        $("#news-card-2").html(newsList[homeStartBox+1]);
-        if(homeStartBox + 2 >= newsList.length){
-            $("#news-right-arrow").removeClass("enabled-news-scroller")
-            $("#news-right-arrow").addClass("disabled-news-scroller")
-        }
-
-        if(homeStartBox == 0 && $("#news-left-arrow").hasClass("enabled-news-scroller")){
-            $("#news-left-arrow").removeClass("enabled-news-scroller")
-            $("#news-left-arrow").addClass("disabled-news-scroller")
-        }
-    }
-    else if($('#news-card-outside-2').css('display') != "none"){
-        // console.log("3 boxes")
-        if(homeStartBox > newsList.length - 3){
-            homeStartBox = newsList.length - 3;
-        }
-        if($("#news-right-arrow").hasClass("disabled-news-scroller")){
-            $("#news-right-arrow").addClass("enabled-news-scroller")
-            $("#news-right-arrow").removeClass("disabled-news-scroller")
-        }
-        $("#news-card-1").html(newsList[homeStartBox]);
-        $("#news-card-2").html(newsList[homeStartBox+1]);
-        $("#news-card-3").html(newsList[homeStartBox+2]);
-        if(homeStartBox + 3 >= newsList.length){
-            $("#news-right-arrow").removeClass("enabled-news-scroller")
-            $("#news-right-arrow").addClass("disabled-news-scroller")
-        }
-
-        if(homeStartBox == 0 && $("#news-left-arrow").hasClass("enabled-news-scroller")){
-            $("#news-left-arrow").removeClass("enabled-news-scroller")
-            $("#news-left-arrow").addClass("disabled-news-scroller")
-        }
-    }
+function testResize() {
+	// console.log("resized");
+	//if became smalle
+	if ($('#news-card-outside-2').css('display') == 'none') {
+		console.log('1 box');
+		if (homeStartBox < newsList.length - 1) {
+			// console.log("does not exxist")
+			if ($('#news-right-arrow').hasClass('disabled-news-scroller')) {
+				$('#news-right-arrow').addClass('enabled-news-scroller');
+				$('#news-right-arrow').removeClass('disabled-news-scroller');
+			}
+		}
+	} else if (
+		$('#news-card-outside-3').css('display') == 'none' &&
+		$('#news-card-outside-2').css('display') != 'none'
+	) {
+		// console.log("2 boxes")
+		if (homeStartBox > newsList.length - 2) {
+			homeStartBox = newsList.length - 2;
+		}
+		if ($('#news-right-arrow').hasClass('disabled-news-scroller')) {
+			$('#news-right-arrow').addClass('enabled-news-scroller');
+			$('#news-right-arrow').removeClass('disabled-news-scroller');
+		}
+		$('#news-card-1').html(newsList[homeStartBox]);
+		$('#news-card-2').html(newsList[homeStartBox + 1]);
+		if (homeStartBox + 2 >= newsList.length) {
+			$('#news-right-arrow').removeClass('enabled-news-scroller');
+			$('#news-right-arrow').addClass('disabled-news-scroller');
+		}
+
+		if (
+			homeStartBox == 0 &&
+			$('#news-left-arrow').hasClass('enabled-news-scroller')
+		) {
+			$('#news-left-arrow').removeClass('enabled-news-scroller');
+			$('#news-left-arrow').addClass('disabled-news-scroller');
+		}
+	} else if ($('#news-card-outside-2').css('display') != 'none') {
+		// console.log("3 boxes")
+		if (homeStartBox > newsList.length - 3) {
+			homeStartBox = newsList.length - 3;
+		}
+		if ($('#news-right-arrow').hasClass('disabled-news-scroller')) {
+			$('#news-right-arrow').addClass('enabled-news-scroller');
+			$('#news-right-arrow').removeClass('disabled-news-scroller');
+		}
+		$('#news-card-1').html(newsList[homeStartBox]);
+		$('#news-card-2').html(newsList[homeStartBox + 1]);
+		$('#news-card-3').html(newsList[homeStartBox + 2]);
+		if (homeStartBox + 3 >= newsList.length) {
+			$('#news-right-arrow').removeClass('enabled-news-scroller');
+			$('#news-right-arrow').addClass('disabled-news-scroller');
+		}
+
+		if (
+			homeStartBox == 0 &&
+			$('#news-left-arrow').hasClass('enabled-news-scroller')
+		) {
+			$('#news-left-arrow').removeClass('enabled-news-scroller');
+			$('#news-left-arrow').addClass('disabled-news-scroller');
+		}
+	}
 }
 
-
-
-
-
 var timeout = false, // holder for timeout id
-delay = 250; // delay after event is "complete" to run callback
+	delay = 250; // delay after event is "complete" to run callback
 
-window.addEventListener('resize', function() {
-    // clear the timeout
-    clearTimeout(timeout);
-    // start timing for event "completion"
-    timeout = setTimeout(testResize, delay);
+window.addEventListener('resize', function () {
+	// clear the timeout
+	clearTimeout(timeout);
+	// start timing for event "completion"
+	timeout = setTimeout(testResize, delay);
 });
 
-window.addEventListener('popstate', function(e) {
-    var location = e.state;
-    if (location != null) {
-        this.location.reload();
-    } 
+window.addEventListener('popstate', function (e) {
+	var location = e.state;
+	if (location != null) {
+		this.location.reload();
+	}
 });
 
-function clearTabs(currentTab){
-    let found = false;
-    $.each(modules, function(key, id) {
-        if(id!=currentTab){
-            $("#"+id+"-tab-anchor").parent().removeClass('active');
-        }
-        else if(id!="apiaccess"){
-            found = true;
-        }
-    });
-    if(found == true){
-        $("#dropdown-tools").addClass("active-link")
-    }
-    else{
-        $("#dropdown-tools").removeClass("active-link")
-    }
-
-    if (headerModules.includes(currentTab)) {
-        $('#module-header').show();
-        document.getElementById("module-help").href = moduleTitleDescription[currentTab][1];
-        document.getElementById("module-title").childNodes[0].nodeValue = moduleTitleDescription[currentTab][0];
-        document.getElementById("module-description").innerHTML = moduleTitleDescription[currentTab][2];
-    }
-    else {
-        $('#module-header').hide();
-    }
-}
-
-$("#news-link").on('click',function(){
-    console.log( $("#news-container").offset())
-    window.scrollTo(0,40000);
-})
-
-const closeBtn = document.querySelector('.close-button')
-const flashBanner = document.querySelector('.popup-flash')
+function clearTabs(currentTab) {
+	let found = false;
+	$.each(modules, function (key, id) {
+		if (id != currentTab) {
+			$('#' + id + '-tab-anchor')
+				.parent()
+				.removeClass('active');
+		} else if (id != 'apiaccess') {
+			found = true;
+		}
+	});
+	if (found == true) {
+		$('#dropdown-tools').addClass('active-link');
+	} else {
+		$('#dropdown-tools').removeClass('active-link');
+	}
+
+	if (headerModules.includes(currentTab)) {
+		$('#module-header').show();
+		document.getElementById('module-help').href =
+			moduleTitleDescription[currentTab][1];
+		document.getElementById('module-title').childNodes[0].nodeValue =
+			moduleTitleDescription[currentTab][0];
+		document.getElementById('module-description').innerHTML =
+			moduleTitleDescription[currentTab][2];
+	} else {
+		$('#module-header').hide();
+	}
+}
+
+$('#news-link').on('click', function () {
+	console.log($('#news-container').offset());
+	window.scrollTo(0, 40000);
+});
 
-closeBtn.addEventListener('click', ()=>{
-  //flashBanner.style.transform = "translateY(-70vh)";
-  flashBanner.style.display="none";
-})
-setTimeout(()=>{
-    //flashBanner.style.transform = "translateY(-70vh)";
-    flashBanner.style.display="none";
-},20000)
+const closeBtn = document.querySelector('.close-button');
+const flashBanner = document.querySelector('.popup-flash');
 
+closeBtn.addEventListener('click', () => {
+	//flashBanner.style.transform = "translateY(-70vh)";
+	flashBanner.style.display = 'none';
+});
+setTimeout(() => {
+	//flashBanner.style.transform = "translateY(-70vh)";
+	flashBanner.style.display = 'none';
+}, 20000);