ASE provides an independent measure of a cis-eVariant’s effect size. We estimated the effects of the primary eVariant for each eGene by applying allelic fold change to ASE measurements (see Methods). Effect size estimates from both total and allele-specific expression approaches were highly correlated (mean Spearman’s ρ =0.82, s.d.= 2%) with an average ratio of eQTL effect sizes to ASE effect sizes of 0.937 (s.d. =6%; Extended Data Fig. 6b, c). This observation suggests that cis-eQTLs and ASE capture the same regulatory effects.
