Cell-specific eQTL more often involve enhancer elements distal to the transcription start site (TSS) when compared to eQTL shared across cell types (7). It is unclear whether eQTL induced by innate immune stimuli show a similar distribution. By analyzing all expression-associated SNPs (eSNPs), we found that the more conditions an eSNP was observed across, the more proximal it was to the TSS (P < 2.2 × 10−16). Even when assessing only significant eSNPs with association below a P < 5 × 10−8 threshold, a similar effect was apparent (P < 2.9 × 10−11). We find that the effect size for an eSNP increases with proximity to the TSS (fig. S5) and that eSNPs that could only be observed after treatment were significantly more distal than those observed in the naïve state (P < 2.2 × 10−16) (fig. S5), consistent with the pattern previously observed with cell type–specific eQTLs.
