To uncover the genetic elements co-regulating these networks we performed expression QTL (eQTL) mapping for each probe-set's expression trait in the saline and S-score data (Table S5). Doing so across both datasets allowed us to assess how the baseline regulatory architecture of the PFC transcriptome is altered by exposure to acute ethanol. Interestingly, the genetic regulatory profiles for the two datasets differed substantially. Although the majority of probe-sets mapped to at least one suggestive eQTL (Table 1), only 6% of eQTL positions were conserved in both the saline and S-score datasets. Indeed, we observed a fundamental shift in the type of genetic regulation most prominent across these datasets. Of the 3,279 genes with significant eQTL in the saline expression data, 42% were considered to be cis-acting, since the peak eQTL location mapped within 5 Mb of the linked expression trait. Whereas in the S-score data cis eQTL accounted for less than 1% of the 1,215 genes with significant eQTL.
