Reads were mapped using Stampy (58), and peaks were called with MACS2 (59) using non-immunoprecipitated DNA as a control for enrichment. Analysis was performed with BEDTools (60). Only peaks found in both samples were used for comparison with trans-associated probes to rs13149699. We observed 481 independent peaks that overlapped by a minimum of 10% in the two biological replicates in the untreated state: 170 after 2-hour LPS2 and 154 after IFNγ stimulation. The number of peaks found within defined distances (as per Fig. 4F) of trans-associated probes was counted and compared to those found within the same distance of non–trans-associated probes that had been similarly tested for eQTL. A Fisher’s exact test was performed to test significance of number of occurrences per genomic window flanking the trans-associated probes versus non-associated probes.
