Pan-cell type continuous chromatin state annotation of all epigenomes from the International Human Epigenome Consortium

The International Human Epigenome Consortium has generated thousands of epigenomic datasets that mea-sure various biochemical activities in the genome, including transcription factor binding, histone modification, and DNA accessibility. Currently, the predominant methods for integrating these datasets to annotate regu-latory elements are segmentation and genome annotation (SAGA) algorithms. The majority of annotations by these methods are cell type-specific. However, as the number of profiled cell types has grown into the thousands, using thousands of cell type-specific chromatin state annotations proves undesirable for many applications. Here, we present a pan-cell type annotation that summarizes all IHEC epigenomes using the recently-developed method, epigenome-ssm.