The Bonferroni adjustment method can be conservative when there is dependence among the expression traits and among the SNP genotypes. Given that strong correlation structures exist among expression traits and among SNP genotypes in a givenlinkage disequilibrium (LD) block, the Bonferroni adjustment may be overly conservative. Therefore, we used an empirical FDR method based on permutations that accounts for the correlation structures among the expression traits and among the SNP genotypes. We constrained the empirically determined FDR to be less than 10% (see Methods). At this level, we identified 3,210 expression traits corresponding to 3,043 genes that were significantly associated with at least one SNP near the corresponding gene region (referred to here as a putative cis eQTL). The full list of association results are provided in Table S2. The magnitude of the effects ranged from SNPs that explained roughly 2% of the in vivo expression variation (p ∼ 0.003) to those that explained roughly 90% of the expression variation (p < 10−65).
