At increasing thresholds for linkage, a higher fraction of detected eQTLs were cis-acting (Figure 4C). The increased proportion of cis-eQTLs with increasing LOD score thresholds has been reported before [5,15] and confirms what is likely to be our increased power to detect first-order cis-acting variations affecting transcription. The proportion of eQTLs with significant sex effects remained relatively constant at all thresholds (Figure 4C). Furthermore, the majority of these sex-specific eQTLs (73%) are acting in trans on a given gene's expression (Figure 4D), and similar proportions of sex-specific eQTLs (26%) are cis compared to the proportion of all liver cis-eQTLs (32%). These data demonstrate the profound effects of sex on the genetic regulation of gene expression.