Extended Data Fig. 5: Associations of SVA F1 insertion and nearby variants to aberrant ASIP splice junction usage in skin and tibial nerve.
From: A sequence of SVA retrotransposon insertions in ASIP shaped human pigmentation
a, Fraction of splice junctions from exon 2 that aberrantly splice into the acceptor site in the nearby SVA F element (versus splicing to exon 3), stratified by SVA F1 insertion genotype in GTEx tibial nerve samples. Only samples with greater than 10 total reads supporting either splice junction are included in the violin plot (n = 33) to reduce noise from less informative points. Centers: combined fraction of aberrant splicing across all samples with each SVA F1 insertion genotype (total n = 532); error bars: 95% CIs from bias-corrected and accelerated bootstrap. b, Local association plot for aberrant splice junction usage in skin (not sun-exposed, NSE) samples (n = 433) in the region 32.5 Mb to 37.5 Mb on chromosome 20. Association strengths track with linkage disequilibrium with the SVA F1 insertion (yellow-to-purple shading), indicated by the large purple dot. c, As in b, but after including SVA F1 genotype as a covariate. d, As in b, but for skin (sun-exposed, SE) samples (n = 497). e, As in d, but after including SVA F1 genotype as a covariate. f, As in b, but for tibial nerve samples (n = 364). g, As in f, but after including SVA F1 genotype as a covariate.
