The modulatory effects of genetic variation on gene expression are seen for specific genes dependent on particular stimuli and the kinetics of the response. We uncover that such genetic effects may only be seen in the early response after induction of expression or less commonly in modulating the extent of subsequent down-regulation. Although we only analyzed two time points for LPS, it is plausible that similar temporal effects exist for IFNγ and other stimuli. We frequently observe pathways where multiple genes show individual and specific associations with particular genetic markers. Although we anticipated that eQTL might manifest only after cellular stimulation in highly inducible genes such as cytokines, as observed in IL1B, IL6, and LTA, less expected was the observation of similar induced eQTL in many upstream nodal genes such as TRAF6 and SOCS1.
