The result remained largely unchanged if the cis-mQTLs were selected at PmQTL < 5 × 10−8 in the LBC data (Supplementary Fig. 15), again showing the robustness of our results to the choice of reference tissue. In addition, of the 5416 cis-mQTLs, 1847 (34%) showed significantly different effects between brain (Jaffe et al.) and blood (LBC) after correcting for multiple testing (Pdifference < 0.05/5416). We then tested whether cis-mQTLs in any of the REMC functional categories tend to have higher TD between brain and blood (see above). There were small but significant enrichments of TD in enhancer regions (e.g., transcribed enhancer, active enhancer and weak enhancer) (Fig. 4c), and one of them survived multiple-testing correction (Supplementary Table 5).
