3C, Figure S5). Based on this observation, we estimated π1 to be 0.41–0.63 when we considered only the closest feature to each xQTL SNP (Figure 3D). Also, we examined the effect of window size by restricting the haQTL analyses to 2Kb, 40Kb, and 100Kb windows as well as changing the eQTL and mQTL analysis window to 100Kb, and found negligible differences in our estimates of xQTL sharing (Table S4).
