ASE can be estimated from the abundance of RNA-seq reads supporting each of the gene’s alleles, measured at heterozygous sites within the transcribed region. We identified a median of 6385 sites per sample (across all tissues and all individuals) that were both heterozygous for a transcript SNP in the imputed genotype data of the associated individual and well expressed in that sample (SNP covered by ≥ 30 RNA-seq reads) (fig. S18). Of these sites, a median of 390 sites per sample had significant ASE (binomial P < 0.005, or 144 sites with FDR 21%, after rigorous quality control of ASE sites and after downsampling to exactly 30 reads at each site to ensure equal power to detect ASE) (Fig. 3A and table S8A) (14). To assess whether different tissues vary in terms of the overall effect of cis-regulatory variation in 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
