The strong correlation of cis-eQTL effects between brain and blood (Fig. 1) does not preclude eQTLs with detectable difference in effect size between tissues. Of the 1388 cis-eQTLs with PeQTL < 5 × 10−8 in GTEx-muscle and available in CMC and GTEx-blood (Supplementary Table 2), 308 (22%) showed significant difference in effect between CMC and GTEx-blood after Bonferroni correction for multiple testing (Pdifference < 0.05/1388) (Methods). Note that the substantial proportion of eQTLs with significant between-tissue differences in effect does not contradict the large estimate of rb above (Fig. 1) because the power to detect a difference in effect depends on sample size13 (Supplementary Fig. 12). Previous studies have indicated that chromatin state at promoters is largely invariant across diverse cell types whereas enhancers are marked with highly cell-type-specific histone-modification patterns27, that functional variants (predicted by chromatin activity data) in enhancers are less likely to be shared across many tissues compared with those in promoters28, and that cell-type-specific eQTLs are more dispersedly distributed around the transcription start site than eQTLs affected expression in multiple cell types29,30. These results seem to
