eQTL are enriched for SNPs that are highly differentiated between European and African populations. FST values for the study SNPs were calculated between 1000 Genomes Project European (EUR) and African (AFR) populations using Weir and Cockerham’s unbiased estimator. SNPs with FST > 0.25 were defined as population differentiated SNPs. (A) The histogram shows the distribution of FST values for the significant colon cis-eQTL (FDR < 0.20). Among the 14,135 cis-eQTL for which FST estimates were obtained, 3,185 (23%) were population differentiated. (B) Enrichment of population differentiated SNPs among significant colon cis-eQTL was evaluated using a simulation-based method. The box plot depicts the distributions of the number of population differentiated SNPs among 1,000 randomly selected cis-eQTL SNP sets (left)―generated by randomly selecting a single SNP for each unique cis-eQTL target gene (n = 684) among all cis-eQTL (FDR < 0.20) that are significantly associated with the expression of that gene―and among 1000 random sets of SNPs (right), each matching the set of 684 significant cis-eQTL SNPs, based on the distributions of MAF and distance from the nearest TSS. The numbers of population differentiated SNPs among the eQTL and random SNP sets are indicated by horizontal lines with the boxes covering 25th and 75th percentiles and the whiskers extending to 1.5 times the interquartile range. The numbers of population differentiated SNPs in the eQTL sets were significantly higher than in the random sets of SNPs (p < 0.001 by Mann–Whitney test).