We also examined effect size estimates for eQTLs that are shared between tissues. The vast majority of shared eQTLs show consistent effect directions in different tissues. However, some SNPs showed apparent opposite effect directions in different tissues (fig. S16). A number of examples that we investigated using multi-SNP multitissue analyses (28) appeared to be due to pairs of SNPs, in LD with one another, that were separate eQTLs in different tissues (fig. S17) rather than being a single eQTL with opposite effects.
