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 highlight that common eQTLs do not explain all of the cis-regulatory effects in individuals and are inadequate predictors of allelic expression variance at the individual level. The higher variance in eQTL heterozygotes than in homozygotes (Mann-Whitney P = 2.13 × 10−7; Fig. 4B) suggests that part of this variance might originate from modification of the main eQTL effect by environmental or trans effects, or due to additional, independent regulatory variants (34).
