Table 2. Melanin index meta-analysis results for suggestively associated SNPs that also nominally replicated.
| SNP | Chromosome band | Position | Nearest gene(s) | A1/A2 | Discovery sample (n = 285) | Replication sample (n = 373) | Meta-analysis | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Freq.a | β (95%CI) b | p-value | Freq.a | β (95%CI) b | p-value | β (95%CI) b | p-value | |||||
| rs79592764 | 3q27.3 | 187398936 | SST-RTP2 | T/C | 0.035 | 6.38 (1.34 to 9.02) | 3.47 × 10−6 | 0.080 | 3.61 (0.48 to 6.73) | 2.43 × 10−2 | 5.23 (3.21 to 7.24) | 3.84 × 10−7 |
| rs35397 | 5p13.2 | 33951116 | SLC45A2 | T/G | 0.511 | −2.49 (−3.53 to −1.45) | 4.19 × 10−6 | 0.217 | −3.29 (−5.35 to −1.24) | 1.81 × 10−3 | −2.66 (−3.58 to −1.73) | 2.05 × 10−8 |
| rs16891982 | 5p13.2 | 33951693 | SLC45A2 | G/C | 0.523 | −2.66 (−3.67 to −1.65) | 4.27 × 10−7 | 0.189 | −3.74 (−5.92 to −1.56) | 8.36 × 10−4 | −2.85 (−3.77 to −1.94) | 9.71 × 10−10 |
| rs6602665 | 10p13 | 13605982 | BEND7-PRPF18 | C/T | 0.079 | 4.72 (2.89 to 6.54) | 7.27 × 10−7 | 0.235 | 3.14 (1.13 to 5.15) | 2.34 × 10−3 | 4.01 (2.66 to 5.36) | 6.14 × 10−9 |
| rs6602666 | 10p13 | 13606490 | BEND7-PRPF18 | G/A | 0.079 | 4.72 (2.89 to 6.54) | 7.27 × 10−7 | 0.237 | 3.20 (1.20 to 5.19) | 1.80 × 10−3 | 4.03 (2.68 to 5.37) | 4.58 × 10−9 |
| rs2675345 | 15q21.1 | 48400199 | SLC24A5 | G/A | 0.277 | 3.31 (2.14 to 4.47) | 5.83 × 10−8 | 0.756 | 5.57 (3.59 to 7.55) | 6.60 × 10−8 | 3.89 (2.89 to 4.89) | 2.98 × 10−14 |
| rs1426654 | 15q21.1 | 48426484 | SLC24A5 | G/A | 0.312 | 3.06 (1.96 to 4.16) | 1.02 × 10−7 | 0.762 | 5.90 (3.91 to 7.89) | 1.31 × 10−8 | 4.36 (1.58 to 7.13) c | 2.62 × 10−14 c |
| rs2470102 | 15q21.1 | 48433494 | SLC24A5 | G/A | 0.277 | 3.31 (2.14 to 4.47) | 5.83 × 10−8 | 0.756 | 5.60 (3.63 to 7.57) | 5.08 × 10−8 | 4.31 (2.08 to 6.53) c | 3.70 × 10−14 c |
| rs8028919 | 15q21.1 | 48460188 | MYEF2 | A/G | 0.793 | −2.95 (−4.22 to −1.68) | 7.99 × 10−6 | 0.385 | −3.96 (5.65 to −2.27) | 6.15 × 10−6 | −3.31 (−4.33 to −2.30) | 1.62 × 10−10 |
| rs11637235 | 15q21.1 | 48633153 | DUT | T/C | 0.509 | −2.26 (−3.24 to −1.28) | 9.61 × 10−6 | 0.183 | −5.71 (−7.93 to −3.48) | 7.76 × 10−7 | −3.83 (−7.20 to −0.46) c | 3.34 × 10−10 c |
| rs2899446 | 15q21.2 | 50307416 | ATP8B4 | G/A | 0.544 | 2.28 (1.34 to 3.21) | 2.73 × 10−6 | 0.783 | 2.30 (0.15 to 4.45) | 3.67 × 10−2 | 2.28 (1.43 to 3.14) | 1.72 × 10−7 |
| rs8033655 | 15q21.2 | 50308950 | ATP8B4 | G/A | 0.544 | 2.28 (1.34 to 3.21) | 2.73 × 10−6 | 0.784 | 2.36 (0.21 to 4.51) | 3.24 × 10−2 | 2.29 (1.43 to 3.14) | 1.54 × 10−7 |
| rs7180182 | 15q21.2 | 50310295 | ATP8B4 | G/A | 0.544 | 2.28 (1.34 to 3.21) | 2.73 × 10−6 | 0.784 | 2.36 (0.21 to 4.51) | 3.24 × 10−2 | 2.29 (1.43 to 3.14) | 1.54 × 10−7 |
| rs6142102 | 20q11.22 | 32704627 | EIF2S2-ASIP | G/C | 0.616 | 2.24 (1.28 to 3.20) | 7.28 × 10−6 | 0.420 | 2.12 (0.42 to 3.82) | 1.52 × 10−2 | 2.21 (1.38 to 3.05) | 2.22 × 10−7 |
aFreq.: Frequency of the effect allele; bEffect size for the effect alleles (additive model); cRandom effect model was used since heterogeneity was found between the discovery and replication samples. Abbreviations: A1: Effect allele; A2: Non-effect allele; CI: confidence interval.