Table 1.
Features of index SNPs in genome regions associated with pigmentation traits in the CANDELA sample
| Trait/Association (P value) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Skin | Hair | Eye | |||||||
| Region | SNP | Candidate gene | SNP annotation | MI | Categorical | Categorical | L (brightness) | C (saturation) | cos(H) (hue) |
| 1q32 | rs3795556 | DSTYK | 3’ UTR | 2.1E-01 | 9.1E-01 | 6.8E-01 | 6.9E-03 | 4.0E-09 | 2.3E-01 |
| 5p13 | rs16891982a,b | SLC45A2 | F374L | 1.3E-117 | 6.3E-66 | 1.3E-15 | 4.0E-17 | 5.4E-07 | 1.8E-04 |
| 6p25 | rs12203592b | IRF4 | Intronic | 3.2E-10 | 2.0E-13 | 1.3E-12 | 3.2E-14 | 1.1E-03 | 4.5E-02 |
| 9p23 | rs10809826a,b | TYRP1 | Intergenic | 1.1E-03 | 3.3E-02 | 1.0E-10 | 5.0E-16 | 2.0E-08 | 1.2E-02 |
| 10q26 | rs11198112 | EMX2 | Intergenic | 1.7E-10 | 6.1E-01 | 3.6E-01 | 4.9E-01 | 7.7E-01 | 4.9E-01 |
| 11q14 | rs7118677a,c | GRM5 | Intronic | 1.1E-09 | 3.1E-06 | 6.1E-01 | 7.5E-01 | 4.8E-01 | 5.5E-01 |
| 11q14 | rs1042602 | TYR | S192Y | 9.1E-10 | 2.3E-06 | 7.5E-01 | 3.9E-01 | 3.6E-02 | 7.8E-01 |
| 11q14 | rs1126809a,c | TYR | R402Q | 2.5E-09 | 6.2E-06 | 1.2E-04 | 5.3E-06 | 7.4E-02 | 7.7E-04 |
| 15q13 | rs4778219c | OCA2 | Intronic | 8.3E-01 | 7.4E-01 | 4.7E-02 | 8.9E-02 | 6.2E-01 | 2.0E-01 |
| 15q13 | rs1800407c | OCA2 | R419Q | 6.5E-09 | 5.5E-02 | 1.1E-02 | 7.2E-02 | 1.4E-07 | 4.8E-06 |
| 15q13 | rs1800404b | OCA2 | Synonymous/TFB | 5.0E-11 | 7.0E-03 | 1.3E-11 | 5.0E-19 | 1.2E-06 | 4.1E-02 |
| 15q13 | rs12913832b | HERC2 | Intronic | 1.0E-17 | 7.9E-105 | 1.0E-200 | 1.0E-200 | 5.7E-07 | 1.3E-92 |
| 15q13 | rs4778249a,c | HERC2 | Intronic | 2.5E-06 | 1.2E-03 | 1.4E-10 | 2.5E-20 | 4.2E-15 | 5.1E-01 |
| 15q21 | rs1426654b | SLC24A5 | T111A | 1.6E-130 | 1.0E-18 | 1.0E-26 | 7.9E-50 | 6.3E-45 | 4.4E-01 |
| 16q24 | rs885479 | MC1R | R163Q | 1.9E-07 | 5.4E-02 | 5.6E-01 | 9.6E-01 | 8.0E-01 | 9.0E-01 |
| 19p13 | rs2240751 | MFSD12 | Y182H | 1.7E-10 | 8.2E-01 | 3.1E-01 | 9.6E-01 | 1.2E-01 | 9.1E-01 |
| 20q13 | rs17422688 | WFDC5 | H97Y | 5.2E-01 | 6.9E-01 | 8.2E-01 | 2.0E-01 | 9.0E-01 | 2.0E-08 |
| 22q12 | rs5756492 | MPST | Intronic | 4.6E-03 | 9.9E-01 | 2.7E-02 | 9.5E-03 | 5.0E-08 | 1.5E-01 |
Novel genomic regions are in bold. Genome-wide significant P values (<5 × 10−8) are in bold and underlined. Genome-wide suggestive significant P values (<10−5) are in bold
MI: melanin index, L: lightness, C: chroma, H: hue
aThese SNPs were obtained through imputation. Their imputation quality ‘info’ metric was ≥0.975, the median value being 0.993. The other SNPs were obtained from chip genotyping, and their ‘concordance’ metric was >0.9, the median value being 0.981
bThese SNPs have been robustly associated with pigmentation traits in previous studies, and they explain a large proportion of the phenotypic variance in our sample (see Methods). These six SNPs were therefore used to condition the GWAS in subsequent analyses
cThe independence of association signals of these SNPs from the main index SNPs in the same regions was confirmed by conditioned analyses