Mediation analysis of local chromatin state and gene expression data in human cell lines.

SNP associations with (a) SLFN5 and (b) GPR63 expression (top) and nearby chromatin accessibility (bottom) for variants on the genes’ chromosome. Peak SNPs are labeled. Mediation results for the (c) SLFN5 eQTL and (d) GPR63 eQTL. Log posterior odds from Bayesian model selection (top), -log10 p-values from Sobel test (middle), and zoomed-in window highlighting gene start, peak SNP, and peak mediator (bottom). Peak mediator or co-local chromatin peak is labeled. Each gray point represents a chromatin peak candidate mediator located near the gene of interest. For SLFN5 expression, complete and partial mediation models were summed in the posterior summary from Bayesian model selection. For GPR63 expression, the co-local model was also summed with the mediation models. Posterior model probabilities from Bayesian model selection for the peak mediator and co-local chromatin peaks and the implied DAG for the (e) SLFN5 eQTL and (f) GPR63 eQTL.