Supplementary Figure 4: Comparison with genome segmentation and the gene body effect on chromatin accessibility.
From: High-resolution genetic mapping of putative causal interactions between regions of open chromatin
(a), Percentage of concordant effect directions between peaks overlapping seven different segmentation annotations. The white dots show the effect direction is significantly higher or lower than the background after multiple-testing correction (q value < 0.05 for the 7 × 7 = 49 tests). (b), 2 by 2 table illustrating the testing for enrichment of peaks within a gene body, downstream of a promoter peak colocalized with the gene. The background is the downstream peak found in a mirrored gene body 5ʹ of the promoter. A promoter peak was defined by colocalizing with the target gene expression QTL (posterior probability > 0.5) and overlapping with the ENCODE active promoter. (c), Scatterplot of the expression level of a gene against average chromatin accessibility in the gene body (n = 20,046 protein-coding genes with one or more chromatin accessibility peaks found within the gene body). The red line shows the regression line (beta = 0.18, P = 2.8 × 10–1,300).
