eQTLs are concentrated near the transcription start and end sites of genes. (A) Distribution of the distance between eQTLs and the closest of the boundaries (TSS or TES) of the gene whose expression they correlated with, for all pairs at 5% FDR. When a gene’s expression correlates significantly with more than one SNP, a single SNP is retained as having either the set of genotypes with the most significant correlation (gray bars) or being the most proximal to one of the two gene boundaries (TSS or TES). (B,C) Quantile-quantile plot of SNP/gene P-values, grouped by distances from the SNP to TSS (B) and TES (C). Selection of P-values to be plotted followed a similar procedure to that in Figure 4B, with all SNPs located up to 250 kb on either side of the gene boundaries or within the gene body included for consideration.