To complement eQTL analysis, we used allele-specific expression (ASE) of genes to indirectly estimate the overall effect of cis-regulatory variants on the expression of nearby genes. Individuals that are heterozygous for a cis-regulatory variant may differentially express each of the two alleles of the affected gene. In these cases, assuming no other causes for allele-specific expression, imbalanced allelic expression of a gene can be used to infer the effect of cis regulation on the gene even without necessarily identifying the specific regulatory variant(s). In addition to the subtle cis-regulatory effects described here, ASE of premature stop variants is also informative of nonsense-mediated decay (31), and consistent monoallelic expression of specific genes can be used to detect epigenetic silencing by imprinting.
