Fig. 3

Chromatin modules capture CREs associated with gene expression. a Schematic representation of how we identified CM and non-CM peaks closest to the gene transcription start site (TSS) to test the strength of association of either peak height or aCM score with closest gene expression. For each gene, the correlations were computed between gene expression and heights of the closest not CM peaks or closest CM peaks or aCM scores. b Violin plots indicating the correlation between each gene expression (for n = 26,362 genes) and the closest CM/not CM peak heights (left panel). Median absolute correlation values per category are closest CM peak, 0.063; closest not CM peak, 0.054; and strongest CM peak, 0.115. Distance to the closest peak center from gene transcription start site (TSS) (right panel). For each CM that had a peak closest to the gene, we also found the best-correlating CM peak, which is indicated as the “strongest CM peak” in light blue. c–e Examples of CMs spanning genes in various cell types having a cmQTL (red triangles). The tracks below CMs and genes show the association strength (adjusted R² (Rsq) of the linear regression) between every peak in the locus and expression of the gene highlighted in dark blue