Although eQTL analysis and other association-based analyses are efficient for identifying common variants with phenotypic effects in populations, the genotype of those variants may not be a good indicator of the gene expression phenotype at an individual level. We investigated this using ASE analysis to estimate how consistent the allelic effect of single-tissue eQTL variants are across individuals that share the same genotype for the best associated eQTL variant per gene. We tested a subset of 606 eQTLs that had high read coverage and a large number of samples for transcript heterozygous sites in the eQTL discovery tissue. We identified 53 eQTLs with significant replication of the eQTL signal in ASE, as inferred by higher allelic imbalance in eQTL heterozygotes than in homozygotes (linear regression P < 0.05 after Bonferroni correction; Fig. 4, A and B). Further, for 22 of the 53 eQTL genes, individuals show variability in their allelic ratios that cannot be accounted for by the eQTL genotype or sampling error (Bonferroni corrected P < 0.05 from permutation of read counts; Fig. 4, C and D). These results
