To determine the effect sizes of cis-eQTLs, we used allelic fold change, a method that assumes an additive model of eQTL alleles on total gene expression, allowing for interpretation of effect sizes as a fold change between alleles27 (Supplementary Information 14). 17.4% of eGenes had cis-eQTLs with median effect sizes of at least twofold across tissues (Extended Data Fig. 11a, c). The prevalence of many ≥ twofold effects highlights the large impacts that common regulatory variants can have on gene dosage. cis-eVariants at canonical splice sites exhibited the strongest effects, followed by variants in noncoding transcripts, while variants in the 3′ UTR had the weakest effects (Fig. 3e).
