Hi-C Aggregate Resource


We provide a Hi-C data aggregate resource. The aggregate is constructed of at least 3500 human, 6600 mouse and 400 drosophila SRA runs.

Full Aggregate for All Resolutions


All genome-wide Hi-C aggregate dataset for a species/resolution combination is available here . The downloaded file is in Hi-C Explorer format. Files range from a few MB to tens of GB, so download times may be long.

Gene Vectors


Obtain the contacts of a gene with the entire genome for various species/resolution combination under the Gene Vector tab. The downloaded vector is a BED file where the coloumns are chrom chromStart chromEnd contact_frequency. This file can be loaded in UCSC genome browser as a custom track


Did you find this app helpful?

If so, please consider citing us at:

Ruchi Lohia, Nathan Fox, and Jesse Gillis
A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships, BioRxiv, March 27 2022,
paper link


Have a question or issue?

Feel free to contact John Lee at johlee@cshl.edu to report an issue, suggest an update, or ask for help.

Download Gene Vector

Gene Vectors for All Resolutions