We searched for eQTL associations of ~5.88 million single nucleotide polymorphisms (SNPs) and ~577 thousand indels (collectively referred to as markers) with 291,705 exon-level and 26,493 gene-level expression profiles (collectively referred to as expression IDs) in each brain region, plus the average across all available regions (referred to as average-all). Using a false discovery rate (FDR) of 1% and defining sentinels as the most associated marker in a set of markers in high linkage disequilibrium (r2 > 0.8), we found 30,333 cis-eQTL and 59,470 trans-eQTL signals (defined as significant sentinel marker–transcript ID pairs). The cis-eQTL signals comprised 90,885 sentinelized subsignals (sentinel marker–expression ID–tissue combinations; Supplementary Table 2) or 2.2 million unsentinelized subsignals. cis-eQTL signals implicated 27,258 sentinel markers (17,814 SNPs plus 9,444 indels) and 21,617 expression IDs corresponding to 8,573 transcript IDs.
