The effective absence of cis eQTL in the S-score data suggests that mechanisms underlying ethanol-responsive gene regulation may fundamentally differ from those governing basal transcription. However, some portion of the basal cis eQTL are likely spurious associations driven by polymorphisms between the B6 and D2 genomes (see Table S8) that affect microarray probe target hybridization [47], [48]. As the impact of such SNP effects should be invariant across the saline vs. ethanol treatment conditions, any spurious cis eQTL would be effectively filtered out of the S-score eQTL results.
