Here we introduce the 3D Genome Browser (http://3dgenome.org), 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.