them, we estimated the proportion of those sites with significant ASE in each of the tissues (combining data from all individuals) (14) and found that the fraction of significant ASE sites varied widely across tissues, with a range of 1.7 to 3.7% (median 2.3%). Brain regions appeared depleted for allelic effects (2.0% ASE in brain versus 2.7% in other tissues combined; P < 2 × 10−16, Fisher’s exact test) (Fig. 3A), consistent with the hypothesis that brain-specific genes exhibit reduced genetic diversity (32). Our results generally support our eQTL findings; in thyroid, where we observed a high number of eQTLs (Fig. 2A), we also see an increased amount of ASE (Fig. 3B). Blood and LCLs have a higher proportion of allelic effects (3.6% versus 2.3% in others; P < 2 × 10−16, Fisher’s exact test) (Fig. 3B), suggesting nongenetic sources of monoallelic expression possibly due to the more clonal nature of these cells (33).
