Table 1.
Allelic associations at vitiligo susceptibility loci following GWAS meta-analysis and replication study
| GWAS123 meta-analysis | GWAS3 replication study | GWAS123 & GWAS3 replication study meta-analysis |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr. | Variant | Position (Build 37) |
Locus | EA/OA | P value | Odds ratio |
P value | Odds ratio |
P value | Odds ratio (95% CI) |
Heritability explained* (%) |
| 1 | rs301807 | 8484823 | RERE | A/G | 1.84 × 10−12 | 1.22 | 4.09 × 10−04 | 1.17 | 4.14 × 10−15 | 1.21 (1.15–1.27) | 0.003 |
| 1 | rs2476601 | 114377568 | PTPN22 | A/G | 2.21 × 10−14 | 1.39 | 1.08 × 10−05 | 1.36 | 1.21 × 10−18 | 1.38 (1.29–1.49) | 0.003 |
| 1 | rs78037977 | 172715702 | FASLG | G/A | 1.39 × 10−13 | 1.33 | 8.95 × 10−05 | 1.29 | 6.74 × 10−17 | 1.32 (1.24–1.41) | 0.003 |
| 1 | rs16843742 | 198672299 | PTPRC | C/T | 8.84 × 10−09 | 0.82 | 1.87 × 10−02 | 0.88 | 1.02 × 10−09 | 0.83 (0.79–0.88) | 0.002 |
| 2 | rs10200159 | 55845109 | PPP4R3B | C/T | 3.35 × 10−13 | 1.48 | 3.70 × 10−07 | 1.55 | 3.73 × 10−19 | 1.51 (1.38–1.66) | 0.003 |
| 2 | rs4308124 | 112010486 | BCL2L11-MIR4435-2HG | C/T | 4.99 × 10−08 | 1.17 | 1.67 × 10−02 | 1.12 | 3.96 × 10−09 | 1.15 (1.10–1.21) | 0.002 |
| 2 | rs2111485 | 163110536 | IFIH1 | A/G | 2.69 × 10−22 | 0.75 | 8.58 × 10−05 | 0.83 | 6.40 × 10−25 | 0.77 (0.73–0.81) | 0.008 |
| 2 | rs231725 | 204740675 | CTLA4 | A/G | 2.25 × 10−08 | 1.18 | 1.57 × 10−03 | 1.16 | 1.49 × 10−10 | 1.18 (1.12–1.24) | 0.002 |
| 2 | rs41342147 | 242407588 | FARP2-STK25 | A/G | 8.03 × 10−07 | 0.80 | 1.25 × 10−03 | 0.80 | 3.70 × 10−09 | 0.80 (0.74–0.86) | 0.003 |
| 3 | rs35161626 | 23512312 | UBE2E2 | I/D | 7.34 × 10−07 | 0.87 | 1.09 × 10−02 | 0.89 | 3.13 × 10−08 | 0.87 (0.83–0.92) | 0.001 |
| 3 | rs34346645 | 71557945 | FOXP1 | A/C | 6.11 × 10−14 | 0.80 | 4.23 × 10−06 | 0.81 | 7.99 × 10−19 | 0.80 (0.76–0.84) | 0.004 |
| 3 | rs148136154 | 119283468 | CD80-ADPRH | C/T | 5.02 × 10−15 | 1.37 | 1.74 × 10−02 | 1.17 | 4.58 × 10−15 | 1.31 (1.22–1.40) | 0.003 |
| 3 | rs13076312 | 188089254 | LPP | T/C | 3.58 × 10−22 | 1.32 | 3.48 × 10−10 | 1.33 | 1.61 × 10−30 | 1.32 (1.26–1.38) | 0.009 |
| 3 | rs6583331 | 196347253 | FBXO45-NRROS | A/T | 1.39 × 10−07 | 0.86 | 3.62 × 10−02 | 0.91 | 2.53 × 10−08 | 0.87 (0.83–0.92) | 0.002 |
| 4 | rs1031034 | 102223386 | PPP3CA | A/C | 4.78 × 10−06 | 0.86 | 2.14 × 10−03 | 0.86 | 3.43 × 10−08 | 0.86 (0.81–0.91) | 0.001 |
| 6 | rs12203592 | 396321 | IRF4 | T/C | 1.03 × 10−09 | 0.77 | 3.17 × 10−08 | 0.68 | 8.86 × 10−16 | 0.75 (0.70–0.80) | 0.001 |
| 6 | rs78521699 | 2908591 | SERPINB9 | G/A | 3.33 × 10−06 | 0.79 | 2.27 × 10−03 | 0.80 | 2.54 × 10−08 | 0.79 (0.73–0.86) | 0.001 |
| 6 | rs60131261 | 29937335 | HLA-A | D/I | 2.63 × 10−48 | 1.53 | 8.01 × 10−20 | 1.54 | 1.56 × 10−66 | 1.54 (1.46–1.61) | 0.016 |
| 6 | rs9271597 | 32591291 | HLA-DRB1/DQA1 | A/T | 3.15 × 10−89 | 1.77 | nd | nd | nd | nd | 0.042 |
| 6 | rs72928038 | 90976768 | BACH2 | A/G | 1.12 × 10−11 | 1.28 | 2.04 × 10−04 | 1.25 | 1.00 × 10−14 | 1.27 (1.19–1.35) | 0.003 |
| 6 | rs2247314 | 167370230 |
RNASET2-FGFR1OP- CCR6 |
C/T | 1.97 × 10−13 | 0.79 | 1.56 × 10−06 | 0.79 | 1.72 × 10−18 | 0.79 (0.75–0.84) | 0.003 |
| 7 | rs117744081 | 29132279 | CPVL | G/A | 3.74 × 10−22 | 1.95 | 1.88 × 10−06 | 1.66 | 8.72 × 10−26 | 1.84 (1.64–2.06) | 0.004 |
| 8 | rs2687812 | 133931055 | TG-SLA-WISP1 | A/T | 1.98 × 10−11 | 1.21 | 1.69 × 10−03 | 1.15 | 2.19 × 10−13 | 1.19 (1.14–1.25) | 0.007 |
| 9 | rs10986311 | 127071493 | NEK6 | C/T | 5.45 × 10−07 | 1.16 | 5.10 × 10−03 | 1.14 | 1.01 × 10−08 | 1.15 (1.10–1.21) | 0.001 |
| 10 | rs706779 | 6098824 | IL2RA | C/T | 1.30 × 10−24 | 0.74 | 9.25 × 10−05 | 0.84 | 7.20 × 10−27 | 0.77 (0.73–0.81) | 0.012 |
| 10 | rs71508903 | 63779871 | ARID5B | T/C | 1.09 × 10−06 | 1.18 | 1.52 × 10−03 | 1.19 | 6.93 × 10−09 | 1.18 (1.12–1.25) | 0.001 |
| 10 | rs12771452 | 115488331 | CASP7 | A/G | 9.16 × 10−08 | 0.83 | 8.42 × 10−06 | 0.79 | 4.43 × 10−12 | 0.82 (0.78–0.87) | 0.002 |
| 11 | rs1043101 | 35274829 | CD44-SLC1A2 | G/A | 2.08 × 10−13 | 1.24 | 4.20 × 10−06 | 1.24 | 5.26 × 10−18 | 1.23 (1.18–1.29) | 0.003 |
| 11 | rs12421615 | 64021605 |
PPP1R14B-PLCB3-BAD- GPR137-KCNK4-TEX40- ESRRA-TRMT112- PRDX5 |
A/G | 3.38 × 10−06 | 0.87 | 3.78 × 10−03 | 0.87 | 4.81 × 10−08 | 0.87 (0.83–0.91) | 0.001 |
| 11 | rs1126809 | 89017961 | TYR | A/G | 7.13 × 10−32 | 0.67 | 2.54 × 10−13 | 0.68 | 1.16 × 10−43 | 0.67 (0.63–0.71) | 0.012 |
| 11 | rs11021232 | 95320808 | Gene desert | C/T | 1.01 × 10−21 | 1.38 | 3.81 × 10−04 | 1.22 | 2.10 × 10−23 | 1.34 (1.26–1.41) | 0.005 |
| 12 | rs2017445 | 56407072 | IKZF4 | A/G | 3.81 × 10−20 | 1.31 | 1.22 × 10−12 | 1.40 | 6.62 × 10−31 | 1.33 (1.27–1.40) | 0.005 |
| 12 | rs10774624 | 111833788 | SH2B3-ATXN2 | A/G | 1.88 × 10−14 | 0.80 | 1.52 × 10−10 | 0.75 | 6.22 × 10−23 | 0.79 (0.75–0.83) | 0.004 |
| 13 | rs35860234 | 43070206 | TNFSF11 | G/T | 2.82 × 10−06 | 1.16 | 3.45 × 10−04 | 1.20 | 4.76 × 10−09 | 1.17 (1.11–1.23) | 0.001 |
| 14 | rs8192917 | 25102160 | GZMB | C/T | 1.37 × 10−10 | 1.23 | 1.23 × 10−06 | 1.29 | 8.91 × 10−16 | 1.25 (1.18–1.32) | 0.002 |
| 15 | rs1635168 | 28535266 | OCA2-HERC2 | A/C | 6.97 × 10−13 | 1.43 | 7.45 × 10−03 | 1.25 | 8.78 × 10−14 | 1.37 (1.26–1.49) | 0.003 |
| 16 | rs4268748 | 90026512 | MC1R? | C/T | 1.63 × 10−20 | 0.73 | 8.23 × 10−15 | 0.66 | 2.88 × 10−33 | 0.71 (0.67–0.75) | 0.013 |
| 17 | rs11079035 | 40289012 | KAT2A-HSPB9-RAB5C | A/G | 3.20 × 10−06 | 1.18 | 3.19 × 10−05 | 1.28 | 6.77 × 10−10 | 1.21 (1.14–1.29) | 0.001 |
| 18 | rs8083511 | 60028655 | TNFRSF11A | C/A | 9.42 × 10−10 | 1.24 | 3.23 × 10−02 | 1.13 | 2.81 × 10−10 | 1.21 (1.14–1.28) | 0.002 |
| 19 | rs4807000 | 4831878 | TICAM1 | A/G | 1.58 × 10−09 | 1.19 | 2.11 × 10−06 | 1.24 | 1.94 × 10−14 | 1.21 (1.15–1.26) | 0.002 |
| 19 | rs2304206 | 50168871 | SCAF1-IRF3-BCL2L12 | A/G | 6.45 × 10−09 | 0.82 | 4.52 × 10−02 | 0.90 | 2.36 × 10−09 | 0.84 (0.80–0.89) | 0.002 |
| 20 | rs6059655 | 32665748 |
RALY-EIF252-ASIP- AHCY-ITCH |
A/G | 3.58 × 10−13 | 0.63 | 3.08 × 10−08 | 0.57 | 1.04 × 10−19 | 0.61 (0.55–0.68) | 0.004 |
| 20 | rs6012953 | 49123043 | PTPN1 | G/A | 1.18 × 10−07 | 1.16 | 1.74 × 10−02 | 1.11 | 9.47 × 10−09 | 1.15 (1.10–1.20) | 0.002 |
| 21 | rs12482904 | 43851828 | UBASH3A | A/T | 5.74 × 10−29 | 1.43 | 1.16 × 10−03 | 1.18 | 5.84 × 10−29 | 1.35 (1.28–1.43) | 0.010 |
| 22 | rs229527 | 37581485 | C1QTNF6 | A/C | 1.40 × 10−24 | 1.34 | 1.15 × 10−07 | 1.27 | 1.14 × 10−30 | 1.32 (1.26–1.38) | 0.006 |
| 22 | rs9611565 | 41767486 | ZC3H7B-TEF | C/T | 1.99 × 10−12 | 0.78 | 3.34 × 10−04 | 0.82 | 3.13 × 10−15 | 0.79 (0.75–0.84) | 0.003 |
| x | rs73456411 | 29737404 | IL1RAPL1 | T/G | 1.57 × 10−07 | 1.72 | 5.90 × 10−03 | 1.62 | 7.34 × 10−10 | 1.77 (1.47–2.13) | 0.001 |
| x | rs5952553 | 49392721 | CCDC22-FOXP3-GAGE | C/T | 1.81 × 10−08 | 0.85 | 3.48 × 10−02 | 0.92 | 1.05 × 10−09 | 0.86 (0.82–0.90) | 0.001 |
*
Heritability explained by all independent signals of the locus. Chr., chromosome; CI, confidence interval; nd, not determined; EA, effect allele; OA, other allele. Bold, novel significant vitiligo susceptibility loci. The chromosome 16 association peak spans a large number of genes, including MC1R.