A thorough understanding of the genetic contribution to complex traits or disease susceptibility is of great biomedical importance, and may allow to prioritize regions for targeted editing of genetic variants that predispose to or are directly causal for onset of disease. However, only a few studies have so far been able to mechanistically disentangle how regulatory variants contribute to variability in human inter-individual disease susceptibility, as most trait-associated variants appear to fall in non-coding, likely regulatory regions of the genome. Classical views postulated that regulatory variation affects the interaction of transcription factors (TFs) with DNA, which locally affects gene expression and chromatin modifications. However, only a small part of inter-individual variable TF binding can be explained by sequence differences in the respective binding sites. Conversely, DNA regions exhibit a high level of local molecular coordination, which are referred to as variable chromatin modules (VCMs) (other names include cis-regulatory domains (CRDs), chromatin nanodomains or microdomains). VCMs comprise coordinated TF binding and modification of histones in confined genomic locations, which collectively define the activity of the entire locus, i.e. the whole VCM. Within these VCMs, genetic variation can impact chromatin accessibility independent of gene expression, and genetic changes in only certain regulatory elements (REs) can control the activity profile of all other molecular phenotypes. Here we have benchmarked and outlined the best practices to infer VCMs from high-throughput epigenomics data. We further show that single-cell epigenomics (via assay for transposase-accessible chromatin with sequencing (ATAC-seq)) may provide a new means to map VCMs from limited input material. Finally, we provide evidence that VCMs are dynamic during cell state changes, even when the underlying regulatory elements may not change in their epigenetic profile.
