Polymorphisms within gene loci implicated in immune responses are associated with a wide range of diseases. Understanding the genetic underpinnings of interindividual variation in immune and inflammatory responses is therefore of fundamental importance. Here, we have assessed the effect of carefully defined innate immune stimuli of high relevance to monocyte activity upon the generation of primary monocyte eQTL, contrasting observations to those in the naïve state. We illustrate how the majority of genes analyzed in monocytes demonstrate an eQTL under at least one condition. The stimuli examined act through well-annotated pathways, causing large-scale changes in gene expression, and are known to affect chromatin remodeling. These two factors together likely underpin the high degree of context specificity observed for induced eQTL. Our data demonstrate that genetic polymorphisms play a significant role in determining the transcriptional response to differing innate immune stimuli in human monocytes and that such effects may be context-specific.
