Table 1.
GWAS meta-analysis, replication, and overall meta-analysis of novel generalized vitiligo susceptibility loci
| GWAS-MA (GWAS 1 + GWAS 2) | Replication study | Overall Meta-Analysis (GWAS 1 + GWAS 2+ replication study) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | SNP | Positional Candidate gene | RA | EA | EAF | P | OR | TREND P | OR | P | OR | Breslow-Day P |
| 2q24.2 | rs2111485 | IFIH1 | G | A | 0.38 | 1.67 × 10−10 | 0.77 | 7.26 × 10−6 | 0.78 | 4.91 × 10−15 | 0.77 | 1.14 × 10−2 |
| rs1990760 | T | C | 0.38 | 2.00 × 10−9 | 0.78 | 1.18 × 10−5 | 0.78 | 9.33 × 10−14 | 0.78 | 2.83 × 10−2 | ||
| 3q13.33 | rs59374417 | CD80 | A | C | 0.13 | 3.97 × 10−7 | 1.33* | 3.02 × 10−4 | 1.33 | 3.78 × 10−10* | 1.34* | 5.41 × 10−1 |
| rs4330287 | C | A | 0.13 | 3.97 × 10−7 | 1.33 | 5.90 × 10−4 | 1.31 | 7.80 × 10−10 | 1.33 | 5.80 × 10−1 | ||
| 4p16.1 | rs11940117 | CLNK | C | T | 0.47 | 9.00 × 10−8 | 1.24* | 3.03 × 10−2 | 1.13 | 1.96 × 10−8* | 1.20* | 3.99 × 10−1 |
| rs16872571 | T | C | 0.56 | 2.50 × 10−7 | 1.23 | 1.54 × 10−2 | 1.16 | 1.56 × 10−8 | 1.21 | 7.31 × 10−1 | ||
| 6q15 | rs3757247 | BACH2 | G | A | 0.47 | 2.14 × 10−5 | 1.18 | 2.91 × 10−4 | 1.22 | 2.53 × 10−8 | 1.20 | 5.16 × 10−1 |
| 8q24.22 | rs853308 | SLA | A | G | 0.48 | 1.14 × 10−6 | 1.21 | 3.24 × 10−3 | 1.18 | 1.58 × 10−8 | 1.20 | 8.33 × 10−1 |
| 10q25.3 | rs3814231 | CASP7 | G | A | 0.25 | 1.20 × 10−5 | 0.81 | 8.80 × 10−4 | 0.81 | 3.56 × 10−8 | 0.81 | 9.77 × 10−1 |
| rs4353229 | T | C | 0.25 | 1.32 × 10−* | 0.84 | 9.10 × 10−4 | 0.81 | 4.35 × 10−7 | 0.83 | 9.18 × 10−1 | ||
| 11p13 | rs736374 | CD44 | G | A | 0.38 | 3.06 × 10−8 | 1.25 | 1.45 × 10−2 | 1.15 | 3.41 × 10−9 | 1.22 | 1.51 × 10−1 |
| rs10768122 | A | G | 0.41 | 6.13 × 10−8 | 1.24 | 5.74 × 10−3 | 1.17 | 1.78 × 10−9 | 1.22 | 1.66 × 10−1 | ||
| 11q21 | rs4409785 | TYR regulation | T | C | 0.19 | 2.26 × 10−10 | 1.36 | 1.58 × 10−4 | 1.30 | 1.57 × 10−13 | 1.34 | 4.63 × 10−1 |
| rs11021232 | T | C | 0.20 | 9.20 × 10−10 | 1.35 | 3.23 × 10−5 | 1.32 | 1.91 × 10−13* | 1.34* | 6.07 × 10−1 | ||
| 12q13.2 | rs1701704 | IKZF4 | A | C | 0.35 | 1.53 × 10−9 | 1.28 | 4.44 × 10−6 | 1.30 | 3.19 × 10−14 | 1.29 | 8.09 × 10−1 |
| rs2456973 | A | C | 0.35 | 1.22 × 10−9 | 1.28 | 4.97 × 10−6 | 1.30 | 2.75 × 10−14* | 1.29* | 8.16 × 10−1 | ||
| 12q24.12 | rs3184504 | SH2B3 | T | C | 0.49 | 1.32 × 10−11 | 0.76 | 2.31 × 10−7 | 0.75 | 2.46 × 10−17 | 0.76 | 1.17 × 10−1 |
| rs4766578 | T | A | 0.48 | 9.10 × 10−12 | 0.76 | 4.07 × 10−8 | 0.73 | 3.54 × 10−18* | 0.76* | 1.01 × 10−1 | ||
| 15q12-13.1 | rs1129038 | OCA2-HERC2 | T | C | 0.27 | 3.23 × 10−7 | 1.26 | 2.06 × 10−2 | 1.14 | 3.91 × 10−8* | 1.22* | 4.66 × 10−1 |
| rs12913832 | G | A | 0.27 | 3.29 × 10−7 | 1.26 | 2.01 × 10−2 | 1.14 | 3.81 × 10−8 | 1.22 | 4.71 × 10−1 | ||
| 16q24.3 | rs4785587 | MC1R | G | A | 0.49 | 1.08 × 10−8 | 0.80 | 1.44 × 10−4 | 0.81 | 6.35 × 10−12* | 0.80* | 7.98 × 10−1 |
| rs9926296 | A | G | 0.46 | 4.34 × 10−11 | 0.77 | 5.16 × 10−4 | 0.82 | 1.82 × 10−13* | 0.79* | 1.35 × 10−1 | ||
| 19p13.3† | rs6510827 | TICAM1 | C | T | 0.41 | 6.98 × 10−6 | 1.20 | 3.87 × 10−3 | 1.17 | 8.80 × 10−8 | 1.19 | 6.37 × 10−1 |
| 22q13.2 | rs4822024 | TOB2 | G | A | 0.21 | 1.02 × 10−7 | 0.76 | 1.54 × 10−3 | 0.81 | 6.81 × 10−10* | 0.78* | 2.00 × 10−1 |
| rs79008 | G | A | 0.19 | 1.44 × 10−6 | 0.78 | 1.13 × 10−3 | 0.79 | 6.19 × 10−9 | 0.78 | 7.95 × 10−1 | ||
This table reports data for newly identified vitiligo susceptibility loci that had P < 1 × 10−4 in the GWAS meta-analysis (GWAS-MA; GWAS1 + GWAS2), P < 0.05 in the replication study, P < 5 × 10−8 in the overall meta-analysis (GWAS1 + GWAS2 + replication study), with consistent effect allele and non-significant Breslow-Day heterogeneity statistics for the ORs across all three studies (P > 1.09 × 10−3). RA, reference allele; EA, effect allele; EAF, effect allele frequency (among all cases and controls).
Imputed from 1000 Genomes Project data.
The association signal at 19p13.3 does not quite achieve the criterion for genome-wide significance but is included for completeness