Fig. 2: GWAS of skin color traits with colocalization results and SNP-based heritability.

a Manhattan plot with −log₁₀ (P) is presented for CIE LAB values of skin color, and genes colocalized in skin tissues are presented below the Manhattan plot. P-values were estimated using a two-sided score test in BOLT-LMM. The red horizontal line corresponds to the genome-wide significance threshold (P = 5 × 10⁻⁸). Genes in green and purple represent previously reported and unreported loci, respectively. Green dots indicate significant loci in at least one GWAS. Boxes in yellow, red, and blue represent significant loci of L*, a*, and b*, respectively; solid boxes indicate genome-wide significant loci and boxes with colored borderlines indicate nominally significant loci (P < 2.17 × 10⁻³, Bonferroni’s correction for 23 significant loci). For the boxes above colocalized genes, solid boxes indicate that a gene was colocalized (PP.H4 > 0.8) with GWAS of the color-corresponding phenotype. b Incremental R² value, defined as the increase in adjusted R² from the linear regression model relative to that from the model with covariates only. The incremental R² of lead SNPs on previously reported loci and on all identified loci are left and right for each trait, respectively. c SNP-based heritability by age group. For each skin color trait, SNP-based heritability of “young age” (<37 years, N = 11,369), “middle age” (37–49 years, N = 17,011), and “old age” (>49 years, N = 14,390) groups are described in order from left to right. Error bars indicate standard errors (SNP-based heritability estimates ± standard error).