The effect of cis-regulatory variation can also be quantified by allele- specific expression (ASE) analyses obtained by measuring the allelic imbalance of RNA-seq reads at transcribed heterozygous sites. A large-scale, multi-tissue resource of ASE estimates complements eQTL mapping by providing access to individual-specific effects, which assists in the interpretation of rare variants, somatic mutations and patterns of imprinting8,13,14. We measured ASE at more than 135 million sites across tissues and donors, with a median of over 10,000 genes quantified per donor (Supplementary Information 11 and Supplementary Fig. 16). In total, 63% of all protein-coding genes could be tested for ASE in at least one donor and tissue, with 54% exhibiting significant allelic imbalance (binomial test, 5% FDR, |effect size| ≥ 1, Extended Data Fig. 6a). Overall, 88% of testable genes had significant allelic imbalance in at least one donor (binomial test, 5% FDR), demonstrating an abundance of cis-linked regulatory effects. Per donor, a median of 1,963 genes had significant allelic imbalance in at least one tissue, with a median of 570 genes where the donor was not heterozygous for a top eVariant, suggesting more complex or rarer regulatory effects at these loci.
