To characterize further the effect that this set of eSNPs has on the liver transcriptional network, we re-analyzed the association results by restricting attention to this panel of SNPs. We again constrained the FDR to be less than 10% with respect to the eSNP set and identified an additional 3,053 expression traits, corresponding to 2,838 genes that were significantly associated with at least one of the eSNPs (Table S2). We assessed the significance of this new set of expression traits by randomly sampling five sets of SNPs from the full set of SNPs typed in the HLC, such that the size and minor allele frequency distribution matched that of the eSNP set. For each of the randomly selected SNP sets, we analyzed the associations between all expression traits and SNPs in this set. The maximum number of associations detected in any of the five sets at a 10% FDR was only 20, and the mean detection rate over all sets was 12. This demonstrates well the biological utility of the eSNP set, given that this set is significantly enriched for
