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.

Downloads

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.

18. Ramirez, F., Lingg, T., Toscano, S., Lam, K., Georgiev, P., Chung, H., Lajoie, B., de Wit, E., Zhan, Y., de Laat, W., Dekker, J., Manke, T., Akhtar, A. High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Mol. Cell 2015 , 60(1), 146-62.

19. Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Mol Cell. 2017 67(6), 1037-1048.

20. Doynova MD, Markworth JF, Cameron-Smith D, Vickers MH, O Sullivan JM. Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. Skelet Muscle 2017 . 5;7(1):5

21. Jiang Y, Loh YE, Rajarajan P, Hirayama T, Liao W, Akbarian S, et al. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet. 2017 49(8):1239-1250.

22. Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos GL, Lubling Y, Xu X, Lv X, Hugnot JP, Tanay A, Cavalli G. Multiscale 3D Genome Rewiring during Mouse Neural Development. Cell. 2017 171(3):557-572.e24.

23. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011 . Jun 19;43(7):630-8.

24. Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell. 2014 Oct 9;159(2):374-387.

25. William W. Greenwald, Joshua Chiou, Jian Yan, Yunjiang Qiu, Ning Dai, Allen Wang, Naoki Nariai, Anthony Aylward, Jee Yun Han, Nikita Kadakia, Laura Regue, Mei-Lin Okino, Frauke Drees, Dana Kramer, Nicholas Vinckier, Liliana Minichiello, David Gorkin, Joseph Avruch, Kelly A. Frazer, Maike Sander, Bing Ren & Kyle J. Gaulton. (2019). Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nature Communications.

26. Nils Krietenstein, Sameer Abraham, Sergey V. Venev, Nezar Abdennur, Johan Gibcus, Tsung-Han S. Hsieh, Krishna Mohan Parsi, Liyan Yang, Rene Maehr, Leonid A. Mirny, Job Dekker, Oliver J. Rando. (2019). Ultrastructural details of mammalian chromosome architecture. bioRxiv. (Micro-C) .

27. Beagrie RA, Scialdone A, Pombo A et al. (2017).Complex multi-enhancer contacts captured by genome architecture mapping. Nature. 543(7646):519-524. (GAM)

28. Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine Disteche, William S. Noble, ZhiJun Duan. (2015). Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells. Nature Methods. (DNase Hi-C)

29. Sofia A. Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M. Lai, Alexander A. Shishkin, Prashant Bhat, Yodai Takei, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Long Cai, Patrick McDonel, Manuel Garber, Mitchell Guttman. (2018). Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus .Cell. (SPRITE)

30. Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Aiden EL et al. (2017). Cohesin Loss Eliminates All Loop Domains. Cell. 171(2):305-320.e24.

31. Barutcu A et al. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun. 2018 Apr 13;9(1):1444. doi: 10.1038/s41467-018-03614-0.

32. Nora et al. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 2017 May 18;169(5):930-944.e22. doi: 10.1016/j.cell.2017.05.004.

33. Yan J et al. Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers. Cell Res. 2018 Feb;28(2):204-220. doi: 10.1038/cr.2018.1.

34. Haarhuis JHI et al. The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension. Cell. 2017 May 4;169(4):693-707.e14. doi: 10.1016/j.cell.2017.04.013.

35. Lin D et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nat Genet. 2018 May;50(5):754-763. doi: 10.1038/s41588-018-0111-2.

36. Johnston MJ, Nikolic A, Ninkovic N et al. (2019). High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma. Genome Res. 2019 Aug;29(8):1211-1222.

37. Jung I, Schmitt A, Diao Y, Lee A, Liu T, Yang D et al. (2019). A compendium of promoter-centered long-range chromatin interactions in the human genome. Nature Genetics. 2019 Sept.

38. Dixon J, Xu J, Dileep V, Zhan Y, Song F, et al and Yue, F. (2018). Integrative detection and analysis of structural variation in cancer genomes. (2018) Nature Genetics. 50,1388-1398.

39. Flavahan WA, Drier Y, Johnstone SE, Hemming ML et al, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GIST. (2019). Nature. 2019 Oct 16.

40. Li Y, He Y, Liang Z, Wang Y et al. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death Dis 2018 Feb 8;9(2):200.

41. Greenwald W, Chiou J, Yan J, Qiu Y, Dai N, Wang A et al. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. (2019). Nat Commun. 2019 May 7;10(1):2078.

42. Kloetgen A, Thandapani P, Ntziachristos P et al. Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia. (2020). Nature Genetics 23 March 2020.

43. Sati S, Bonev B, Szabo Q Jost D et al. 4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. (2020). Molecular Cell 7 May 2020.

44. Barutcu A, Lajoie B, McCord R et al. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. (2015). Genome Biology 28 Sep 2015; DOI 10.1186/s13059-015-0768-0.

45. Wu P, Li T, Li R, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y & Li C. 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. 2017. Nat Commun 05 Dec 2017.

46. Heinz S, Texari L, Hayes MGB, Urbanowski M et al. Transcription Elongation Can Affect Genome 3D Structure. (2018) cell 6 Sep 2018; 174(6):1522-1536.e22.

47. Taberlay P, Achinger-Kawecka J, Lun A et al. Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations. (2016). Genome Research 06 Apr 2016.

48. ENCODE Project Consortium.. An integrated encyclopedia of DNA elements in the human genome. Nature 6 Sep 2012; 489(7414):57-74.

49. Guo Y, Xu Q, Canzio D, Shou J et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 13 Aug 2015; 162(4):900-10.

50. Arvanitis M, Tampakakis E, Zhang Y, Wang W et al. Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. (2020) Nat Commun 2020 Feb 28; 11(1):1122.

51. Shoshani O, Brunner S, Yaeger R et al. Chromothripsis drives the evolution of gene amplification in cancer. (2020). Nature 23 Dec 2020.

52. Khattabi L, Zhao H, Kalchschmidt J et al. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. (2019). Cell 22 Aug 2019.

53. Yang J, McGovern A, Martin P, Duffus K, Ge X, Zarrineh P, Morris A, Adamson A, Fraser P, Rattray M, Stephen Eyre S. Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis. (2020). Nat Commun 02 Sep 2020.

54. Cremer M, Brandstetter K, Maiser A et al. Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. (2020). Nat Commun 01 Dec 2020

55. Iyyanki T, Zhang B, Wang Q, Hou Y, Jin Q, Xu J, Yang H, Liu T, Wang X, Song F, Luan Y et al. Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. (2021). Genome Biology 2021

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