Our screen for (cis-acting) polymorphisms controlling expression and splicing evaluated SNPs in or near (within 100 kb) either the target gene or exon. We limited this screen to SNPs with a minor allele frequency (MAF) > 0.04 in our sample sets (requiring at least six alleles to be present in the tissue type investigated). The screen for cis-acting sites controlling overall expression and those regulating exon expression levels required approximately ten and 85 million tests, respectively. On average 40 SNPs were considered for each of the ∼22,000 genes, including ∼12 transcripts per gene and ∼four exons per transcript. Thus, thresholds for study-wide significance were 5 × 10−9 for transcript level associations and 6 × 10−10 for exon-level associations. We identified 584 study-wide significant eQTLs meeting the MAF requirements, but many of these were associated with one another and therefore appeared to reflect the same causal eQTL. We used stepwise regression to eliminate associated SNPs, separately evaluating the two tissue types, and identified 81 independent eQTLs. Significant associations that overlapped between the two tissue types were merged, resulting in 77 transcript
