A GWAS meta-analysis of vitiligo was performed in individuals of non-Hispanic European ancestry across, in total, 3187 cases and 6723 controls. Firstly, a discovery phase  meta-analysis was carried out incorporating two GWAS (GWAS1 1297 Cases and 2235 Controls and GWAS2 450 Cases  (657,366 SNPs Illumina Human660W) and 3182 Controls (Illumina 1Mv1 and 610-Quad BeadChips)). Results were analysed in PLINK with  adjustment for population stratiication using EIGENSOFT.  An independent replication study accross 46 SNPs in 1440 cases and 1316 controls, using a custom Illumina GoldenGate assay identified 13 novel vitiligo associated loci, as well as confirming previous susceptibility loci, at a threshold p.combined<5x10-8 . To further analyse all susceptibility regions genotypes were imputed using MACH (version 1.0) and 1000 Genomes project data (August 4th 2010 release).  Thus, exluding MHC, 23 confirmed vitilgo susceptibility loci are now described

Study Type
Whole Genome Association Study
Exclusion Criteria


  • IBD pi-hat>0.05
  • Call rate <98.5%
  • Hispanic or Non-European ancestry as identified by EIGENSOFT


  • MAF < 0.01
  • HWE deviation P < 10-5
  • Significant missingness between cases and controls P<10-5
  • Manual inspection of allele cluster plots and MAF.cases and MAF.controls for SNPs P<5x10-5

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113296527-114009223PTPN22  rs2476601G > A0.1006.10e-13C 
1p36.23chr1:8307644-8922212RERE  rs4908760A > G0.4003.54e-14C 
2q24.2chr2:162104363-162502867IFIH1  rs2111485G > A0.3804.91e-15C1.3D
3p13chr3:71383727-71585992FOXP1  rs17008723T > G0.1804.81e-08C 
3q13.33chr3:119395846-119595580CD80  rs59374417A > C0.1303.78e-10C1.33D
3q28chr3:188351572-188422865LPP  rs1464510G > T0.4608.83e-20C 
4p16.1chr4:10696641-10911959CLNK  rs11940117C > T0.4701.96e-08C1.24D
6q15chr6:90097116-90317592BACH2  rs3757247G > A0.4702.53e-08C1.18D
6q27chr6:166932351-167134466RP11-517H2.6  CCR6  rs6902119T > C0.4603.81e-08C 
8q24.22chr8:132673404-132969501SLA  rs853308A > G0.4801.58e-08C1.21D
10p15.1chr10:5988280-6129961IL2RA  rs706779A > G0.4504.98e-14C 
10q25.3chr10:113580900-113828180CASP7  rs3814231G > A0.2503.56e-08C1.23D
11p13chr11:35217031-35381990CD44  rs736374G > A0.3803.41e-09C1.25D
11q14.3chr11:89022180-89390600TYR  rs1393350G > A0.2509.32e-18C 
11q21chr11:95537638-95599614TYR  rs4409785T > C0.1901.57e-13C1.36D
12q13.2chr12:55958153-56397446IKZF4  rs1701704A > C0.3503.19e-14C1.28D
12q24.12chr12:111278572-112592683SH2B3  rs3184504T > C0.4902.46e-17C1.32D
14q12chr14:24435396-24698305GZMB  rs8192917A > G0.2505.60e-09C 
15q13.1chr15:28078624-28634439OCA2  HERC2  rs1129038T > C0.2703.80e-08C1.26D
16q24.3chr16:89591311-89947549MC1R  rs4785587G > A0.4906.35e-12C1.25D
19p13.3chr19:4755166-4854638TICAM1  rs6510827C > T0.4108.80e-08C1.20D
21q22.3chr21:42389309-42458550UBASH3A  rs11203203G > A0.3905.81e-12C 
22q12.3chr22:37171497-37262659C1QTNF6  rs229527G > T0.4406.53e-17C 
22q13.2chr22:40723547-41966556TOB2  rs4822024G > A0.2106.81e-10C1.32D
MHCchr6:32393692-32706866rs532098C > T0.4801.60e-52C 
MHCchr6:29904646-30108241HLA-A  rs12206499A > G0.3102.55e-30C 
MHCchr6:32242186-32616832BTNL2  rs3806156G > T0.3901.59e-25C 


GDXHsS00036 meets the following criteria:

Criteria Name
Disease Tags
Study for a Disease 


PMIDTitleFirst AuthorJournalDisease(s)Date