factors including REL-A (nuclear factor κB p65) (fig. S10). In the stimulated cells, this SNP is associated with a major trans network, and on single SNP analysis, more than 300 trans genes were defined in the complete data sets (Fig. 4, C to E, and table S4). Analysis of paired samples showed no probes associating in the naïve cells, implicating treatment-induced differential expression of IRF2 at rs13149699 as the driver of the trans network. IPA of rs13149699 trans-associated genes supported their modulation by IRF2 and interferon signaling, with overrepresentation of interferon-associated pathways and IRF2 identified as an upstream regulator (P = 7.9 × 10−11).
