Eukaryotic chromosomes are a highly organized three-dimensional entity. Chromosome folding is a tightly regulated process1,2, with important functions including bringing distal regulatory elements into the vicinity of their target gene promoters and arranging the chromosomes into distinct compartments. Mapping and visualizing higher order chromatin interactions are critical to genomics research, especially for interpreting high-throughput epigenomic data3–6. Recent technological innovations, including 5C, Hi-C, and ChIA-PET, have facilitated discovery of chromosomal organization principles and folding architectures at unprecedented scales and resolution. Each technology also comes with corresponding computational tools7,8 to process and visualize its specific data type (Supplementary Notes). However, visualizing and navigating long-range interaction data, as well as integrating these interactions with other epigenomics data, remain a much-desired capability and a daunting challenge9.
