In agreement with recent findings in lymphoblastoid cell lines (LCLs)21, we found that a majority of sQTLs act independent of gene expression effects, as evident by the low degree of sharing between sQTLs and eQTLs29 from the same brains (π1 = 0.18) (Fig. 3c). Of the 9,045 lead sQTL SNPs, only 42 are also a lead eQTL, suggesting that a substantial fraction of sQTLs are unique and are not detected by standard eQTL analysis.
