Fig. 5: Comparison of lead variants for L* and polygenic score performance with the UK Biobank.

a Comparison of lead variants for L* from the current GWAS with the UK Biobank European GWAS (top left) and East Asian GWAS (top right), and comparison of lead variants for light skin from the UK Biobank European GWAS with the current GWAS (bottom left) and UK Biobank East Asian GWAS (bottom right). Dots in red, yellow, and gray represent genome-wide significant (P < 5 × 10⁻⁸), nominally significant (P < 2.17 × 10⁻³, Bonferroni’s correction for 23 significant loci), and non-significant variants in the compared GWASs, respectively. Dots in black represent variants without results in the compared GWASs and are plotted along the x-axis. Colocalized genes in skin tissues are marked with an asterisk. Spearman’s correlation (r_s) between effect sizes (β) of variants without black dots is presented at the top of each plot. b Distribution of polygenic score in the UK Biobank East Asian sample. The polygenic scores were calculated with weights from the current GWAS (top) and the UK Biobank European GWAS (bottom). For each decile or quartile of the polygenic score distribution, the proportion of participants who answered dark, intermediate, and light skin color is presented in order from left to right. Spearman’s correlation (r_s) between the residual of polygenic score (adjusted for age, sex, and the first 10 PCs) and skin color and P-values are presented at the top of each plot. The P-value of Spearman’s correlation coefficient was estimated using a two-sided test under the null distribution of all possible permutations.