Fig. 1

Systematic mapping of chromatin modules (CMs) in LCLs. a Schematic representation of ChIP-seq profiles (H3K27ac in green, H3K4me1 in purple) for individuals with differential chromatin activity at the loci. ChIP-seq peaks are shown with purple and green rectangles, where color indicates different histone modifications. Only covariable peaks are used to define a CM, which is depicted with black rectangles at the bottom of the panel. b Schematic representation of the pipeline. We collected available H3K27ac and H3K4me1 ChIP-seq data for LCLs and associated genotypes for 317 individuals. We then used the data to map covariable regions with three approaches: correlation-based approaches (VCMtools, Clomics) that depend only on the epigenome data for CM mapping, and a Bayesian hierarchical method (PHM) that requires genotype information in addition to epigenome data. c The depicted UpSet plot shows the percentage of overlapping CM pairs by at least one base pair across different methods. Left panel: example of the most reproducible CMs across three methods in the MD21D2 gene locus. The top track represents peak-to-peak correlations in the locus. The tracks below show CMs mapped with Clomics (gray), VCMtools (orange), and PHM (green). The bottom tracks show ChIP-seq tracks for two individuals with the most differential CM signal (H3K27ac in dark green, H3K4me1 in dark blue). Right panel: example of the Clomics-specific CM (in gray) in the SPIC gene locus. The top track represents peak-to-peak correlations; the bottom tracks show ChIP-seq tracks for two individuals with the most differential CM signal