Journal article Open Access

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

Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank NK; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, Feng

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.

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