A diverse set of immune-related genes were found to show eQTL after induction with LPS or IFN-γ, ranging from transcription factor genes such as ETS2, JUN, and IRF2 (interferon regulatory factor 2) to key cytokines and receptors such as IL8 (interleukin-8), IL32, IL18R1, and FAS (table S2). For LTA, an eQTL was observed after 2-hour LPS, whereas no eQTL was apparent for TNF on induction at 2 hours but was seen on down-regulation after 24-hour LPS (Fig. 1D). We investigated the relationship of specific treatments with observed eQTLs in terms of canonical gene pathways. This resolved contiguous pathways of induced eQTL activity (fig. S7). For the TLR4 pathway, eQTL specific to treatment were revealed for nodal genes including TIRAP, TRAF6, FADD, and MAP (mitogen-activated protein) kinase genes, whereas genes encoding key components of the inflammasome such as CASP1 and PYCARD, as well as downstream cytokines including IL6, CXCL9, and IFNB1, showed eQTL specific to early and late responses to LPS (Fig. 1E). Similarly, treatment revealed eQTL in nodal IFN-γ signaling pathway genes and many downstream genes involved in the proteasome, apoptosis, antigen processing, and presentation (Fig. 1F).
