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Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C) data. HiC-3DViewer is an interactive chromatin visualization tool that maps genome-scale interactions to identify structural characteristics and interactions between all chromosomes. It allows user to highlight any specific genomic regions through the usage of an interactive 2D Hi-C contact map or by uploading a BED file of given regions.

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HiC-3DViewer classification

HiC-3DViewer specifications

Web user interface
Programming languages:
Javascript, Python
Restrictions to use:
Computer skills:

HiC-3DViewer distribution


HiC-3DViewer support


  • Juntao Tony Gao <>
  • Michael Zhang <>


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MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing, China; Department of Automation, Tsinghua University, Beijing, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA

Funding source(s)

Supported by State Key Research Development Program of China (No. 2016YFC1200303), and the National Natural Science Foundation of China (Nos. 31361163004 and 31671383).

Link to literature

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