Most chromatin interactions are not in linkage disequilibrium

(A) B cell eQTLs (Fairfax et al. 2012) are significantly enriched in statistically significant B cell PCHi-C interactions (Javierre et al. 2016) at both proximal (<200 kb) and distal (200 kb to 2 Mb) distances from their promoters, with an odds ratio of ∼20 (natural log odds ratio of ∼3). (B) eQTLs are significantly enriched only at proximal distances and with smaller odds ratios (∼4) when conditioning on bait fragments containing the closest gene to the promoter-interacting fragment, or (C) conditioning on interacting fragments being in strong LD (maximum pairwise R² > 0.8 for any super-population) with bait fragments. Whiskers are 95% confidence intervals.