We compared the 2102 modQTLs with eQTLs discovered by both the single-tissue and multitissue eQTL analyses. At all correlation levels of stringency, the modQTLs capture 53% of tissue-specific eQTLs (calculated as the percentage of lead SNPs in LD r2 > 0.8 with lead modQTLs) and 60% of multitissue eQTLs, and these two together account for only 42% of modQTL SNPs. Hence, 58% of modQTLs are not discovered by other methods, which suggests that the approach has the potential to reveal novel genetic effects on the modulation of genes across tissues (fig. S31C).
