To further investigate the relationship between innate immune stimuli–induced eQTL and human disease risk loci resolved by GWAS, we first defined independent associations to the same probe interrogating gene expression within and between treatments. To do this, we resolved SNPs associated with the same eQTL into independent peaks of association among the shared data set of 228 individuals by conditional analysis (17). This revealed that although the majority of probes associated with a single peak, 9.8% of probes had a second peak in naïve monocytes, with up to three peaks in a small number of instances (Fig. 5A). Similar proportions were observed after treatment, the number of probes with two peaks modestly increasing to 11% after IFN-γ treatment. Considering all probes with a peak in the naïve state, additional peaks specific to stimulation were found, most markedly after IFN-γ treatment (Fig. 5B).
