The identification of genes underlying cQTLs remains a challenge. The widespread availability of genome-wide expression analysis has begun to address this by providing a snapshot of transcription in relevant organs and thus providing initial information for which genes can differentiate a given trait. Furthermore, by treating transcript levels as quantitative traits, we can map the genetic regulation underlying differential gene expression (eQTLs). Those eQTLs that have cis-acting variations affecting their transcription are potential candidate genes for the trait. At a single trait, genome-wide significance level of 0.05, we detected 6,676 eQTLs representing 4,998 genes, of which 2,118 were cis-acting. At increased thresholds, the proportion of cis-eQTLs increased, which is in good agreement with previous studies [5,15] and likely reflects the increased power to detect cis-acting variations affecting transcription. Of all 6,676 significant eQTLs, 1,166 possessed significant sex interactions. Of these, 304 were cis and 852 were trans, suggesting that only a minority of the sex-specific effects on the regulation of gene expression occur through polymorphisms within the gene itself. Rather, underlying genetic regulation of most transcripts is the result of interactions between trans loci and sex-specific factors (e.g., hormones). As with cQTLs, sex bias in the predominantly trans genetic regulation of gene expression is likely secondary to different sex hormone profiles.