Extended Data Fig. 6: Positive selection signals across cell types and populations.

a, Fold-enrichments (FE) of eQTLs in local adaptation signals across the 22 cell types. Adaptive loci are defined separately in Central Africans (YRI), West Europeans (CEU) and East Asians (CHS), based on the population branch statistic (top 1% PBS). Occurrence of adaptive signals at reQTLs is compared to randomly selected variants, matched for MAF, distance to nearest gene, and LD score. b, Allele frequency trajectories over the past 2,000 generations in YRI (green) and CEU (yellow) of the GBP7 reQTL (rs1142888-G). Lines indicate the maximum a posteriori estimate of allele frequency at each epoch in each population; shaded areas indicate the 95% CIs around these estimates (2.5^th −97.5^th percentiles of posterior distribution). c, Fold-enrichments (FE) of eQTLs and reQTLs in local adaptation signals (top 1% PBS), for eQTLs and reQTLs relative to random variants, matched for MAF, distance to nearest gene, and LD score. reQTLs are analysed either for each stimulus separately (reQTL) or splitting into stimulus-specific and shared reQTLs (reQTL breakdown). a and c. Data are presented as the mean and 2.5^th −97.5^th percentiles (95% CIs) of FE observed over N = 10,000 resamplings.