How to Cite Our Work
Figures generated in this website can be directly used in your publication. If you do, please cite this manuscript.
Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M.N.K., Li, Y., Hu, M., et al. (2018). The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biology. 19, 151. https://doi.org/10.1186/s13059-018-1519-9.
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TADs in hg19 TADs in hg38 TADs in mm9 TADs in mm10 File information
Note: the TADs coordinates provided here are predicted using our in-house pipeline from Dixon et al. Nature 2012 and the list of tissue/cell type will be constantly updated as we add more data. Data source of TAD files can be found in the File information link. Please contact us if you have any quesitons.
Chromatin loops in hg19
Loops in hg38
Loops in mm9
Loops in mm10
Note: Chromatin loops in 56 tissue/cell types were predicted by Peakachu. Please cite our preprint: A supervised learning framework for chromatin loop detection in genome-wide contact maps. [Github]
Source of data available for visualization
We are hosting all the Hi-C and ChIA-PET datasets produced by the ENCODE Consortium. You can also visualize and explore the chromatin interaction data from the following publications. If you have suggestions of datasets to be added to this browser, please contact us.
1. Lieberman-Aiden, E., Nynke L. van Berkum, Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S. & Dekker, J. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science. 2009. 326(5950):289-293. Pubmed Paper Dataset
2. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-380. Pubmed Paper Dataset
3. Shen, Y., Yue, F., McCleary, D., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. & Ren, B. A map of the cis-regulatory sequences in the mouse genome". Nature. 2012;488(7409):116-120. Paper Dataset
4. Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S. & Aiden-Lieberman, E. 2014,. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159(7):1665-1680. Pubmed Paper Dataset
5. Heidari, N., Phanstiel, D.H., He, C., Grubert, F., Jahanbani, F., Kasowski, M., Zhang, M., Snyder, M.P. Genome-wide map of regulatory interactions in the human genome. Genome Research. 2014 Dec; 24(12): 1905-1917. Pubmed
6. Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518(7539):331-336. Pubmed Paper Dataset
7. Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A. Y. & Ren, B. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015;518(7539):350-354. Pubmed Paper Dataset
8. Nagano, T., Lubling, Y., Yaffe, E., Wingett, S. W., Dean, W., Tanay, A., & Fraser, P. Single-cell hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nature Protocols. 2015;10(12):1986-2003.
9. Mifsud, B., Tavares-Cadete, F., Young, A., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S., Andrews, S., Grey, W., Ewels, P., Herman, B., Happe, S., Higgs, A., LeProust, E., Follows, G., Fraser, P., Luscombe, N. & Osborne, C. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nature Genetics. 2015;47(6):598-606. Pubmed Paper Dataset
10. Tang, Z., Luo, O., Li, G., Li, X., Zheng, M., Zhu, J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., Michalski, P., Piecuch, E., Wang, P., Wang, D., Tian, S., Penrad-Mobayed, M., Sachs, L., Ruan, Y., Ruan, X., Wei, C., Liu, E., Wilczynski, G. & Plewczynski, D. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 2015, 163(7), p1611-1627. Paper
11. Schmitt, A., Hu, M., Jung, I., Xu, Z., Qiu, Y., Tan, C., Li, Y., Lin, S., Lin, Y., Barr, C. & Ren, B. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Reports. 2016;17(8):2042-2059. Pubmed Paper Dataset
12. Javierre, B., Burren, O., Wilder, S., Kreuzhuber, R., Hill, S., Sewitz, S., Cairns, J., Wingett, S., Várnai, C., Thiecke, M., Burden, F., Farrow, S., Cutler, A., Rehnström, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F., Stunnenberg, H.G., Todd, J.A., Zerbino, D.R., Stegle, O., Ouwehand, W.H., Frontini, M., Wallace, C., Spivakov, M. & Fraser, P., Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell. 2016;167(5):1369-1384.e19. Pubmed Paper
13. Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A.D., and Ren, B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016 Dec;26(12):1345-1348. Paper Dataset
14. Mumbach, M.R., Rubin, A.J., Flynn, R.A., Dai, C., Khavari, P.A., Greenleaf, W.J. & Chang, H.Y. 2016, HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods.2016;13(11):919-922. Paper
15. Won, H., Torre-Ubieta, L., Stein, J.L., Parkshak, N.N., Huang, J., Opland, C.K., Gandal, M.J., Sutton, G.J., Hormozdiari, F., Lu, D., Lee, C., Eskin, E., Voineagu, I., Ernst, J., & Geschwind, D.H., Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. 2016,538, 523-527. Paper Dataset
16. Jin, F., Li, Y., Dixon, J., Selvaraj, S., Ye, Z., Lee, A., Yen, C., Schmitt, A., Espinoza, C., & Ren, B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013 , 503(7475), 290-4.
17. Rubin, A., Barajas, B., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M., Howard, I., .., Chang, H., Fraser, P., Khavari, P. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat. Genet 2017 , 49(10), 1522-1528.
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