Fig. 2: Association of SVA F1 insertion with pigmentation phenotypes in UKB.
From: A sequence of SVA retrotransposon insertions in ASIP shaped human pigmentation
a, Genotyping of 199,956 UKB participants with WGS. Three genotype clusters corresponding to the dosage of the SVA F1 insertion are apparent. b, Genotype concordance of 917 sibling pairs sharing both ASIP haplotypes IBD2. All but one of the sibling pairs agree on the genotype call made for the SVA F1 insertion. c, Associations of genome-wide imputed SNP and indel variants with self-reported skin color, coded on a scale from fairest to darkest (n = 167,568); P values are from linear regression. The association of the SVA F1 insertion is plotted in purple. d, Local association plot for skin color (n = 167,568) at the extended ASIP locus. Association strengths track with LD with the SVA F1 insertion (yellow-to-purple shading), indicated by the large purple dot. e, Associations at ASIP with any type of skin cancer (C43 or C44 ICD-10 code; ncontrols = 154,340 and ncases = 15,295). f, ORs for skin cancer risk for individuals heterozygous (n = 31,932) or homozygous (n = 1,952) for the SVA F1 insertion relative to individuals homozygous for no insertion (n = 135,751). Centers, effect size estimate for each genotype from logistic regression; error bars, 95% CIs.
