Table 2. Model-based genotype–phenotype association for four pigmentation traits for stage 1.
| Trait | SNP (gene) | p (padj) | OR (95%CI) | Explained heritabilitya |
|---|---|---|---|---|
| Eye colour (blue) dichotomous | rs12913832 (HERC2) | <1.0 × 10−5 (1.2 × 10−4) | 40.0 (18.3–87.5) | 46% |
| rs1800407 (OCA2) | 0.0014 (0.017) | 4.9 (1.8–13.6) | 1% | |
| Hair colour (red tint) dichotomous | rs1805007 (MC1R) | <1.0 × 10−5 (1.2 × 10−4) | 5.4 (2.8–10.3) | 14% |
| rs1805008 (MC1R) | 1.0 × 10−4 (0.0012) | 3.5 (1.9–6.6) | 7% | |
| Hair colour (light-dark, I–IX)b ordinal | rs12913832 (HERC2) | <1.0 × 10−5 (1.2 × 10−4) | 2.9 (1.9–4.4)c | 5% |
| rs12203592 (IRF4) | <1.0 × 10−5 (1.2 × 10−4) | 3.6 (2.0–6.3)c | 5% | |
| Skin type (I–IV) ordinal | rs1805008 (MC1R) | 6.0 × 10−5 (7.2 × 10−4) | 3.0 (1.8–5.1)c | 8% |
| rs1805007 (MC1R) | 0.0035 (0.042) | 2.5(1.4–4.3)c | 5% | |
| rs4778138 (OCA2) | 4.9 × 10−4 (0.0059) | 3.2 (1.6–6.2)c | 4% |
Abbreviations: CI, confidence intervals; OR, odds ratio; SNP, single-nucleotide polymorphism.
padj: Bonferroni-adjusted P-value (adjusted for 12 tests).
a
The proportion of the trait heritability explained by a given variant on the liability scale was assessed as described by So et al41 (without consideration of other markers interacting or in LD).
b
In the analysis of the light-dark component of hair colour, two individuals with pure red hair colour were removed.
c
ORs for ordinal phenotypes correspond to a proportional odds model.