The locations of all SNPs tested in the eQTL analysis are shown in gold relative to the 5′ most gene transcription start site (TSS) and the 3′ most gene transcription end site (TES) for all 10,409 genes. SNPs detected as eQTL are overplotted in blue, and are enriched, relative to all SNPs tested, near transcription start sites, transcription end sites, and within gene bodies. Gray shaded rectangle denotes the region bounded by the TSS and TES, with gene lengths divided into 20 bins for visibility (because the gene body is thus artificially enlarged, SNP density within genes cannot be directly compared with SNP density outside of genes). Note that SNPs that fall outside of one focal gene may fall within the boundaries of other genes. Inset: distribution of all SNPs tested relative to the location of genes, highlighting the concentration of SNPs in genes (the peak at the center of the plot). See Figure 1—figure supplements 1–14 for additional details on workflow, variant calling validation, location of all analyzed SNPs relative to genes, agreement between eQTL and ASE detection, and effects of local structure.