The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Genome Biol. 2018 Oct 4;19(1):151. doi: 10.1186/s13059-018-1519-9.


Here, we introduce the 3D Genome Browser, , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / metabolism*
  • DNA, Intergenic / genetics
  • Databases, Genetic
  • Deoxyribonuclease I / metabolism
  • Genetic Variation
  • Genome, Human*
  • Humans
  • Imaging, Three-Dimensional*
  • Mice
  • Neoplasms / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Species Specificity
  • Web Browser*


  • Chromatin
  • DNA, Intergenic
  • Deoxyribonuclease I