Broad ChromHMM Track Settings
ENCODE Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH   (All Regulation tracks)

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  Cell Line GM12878 (Tier 1)  H1-hESC (Tier 1)  K562 (Tier 1)  HepG2 (Tier 2)  HUVEC (Tier 2)  HMEC  HSMM  NHEK  NHLF Cell Line  
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 GM12878  ENCODE Broad Chromatin State Segmentation by HMM (in GM12878 cells)    Schema   2011-01-21 
 H1-hESC  ENCODE Broad Chromatin State Segmentation by HMM (in H1-hESC cells)    Schema   2011-01-21 
 K562  ENCODE Broad Chromatin State Segmentation by HMM (in K562 cells)    Schema   2011-01-21 
 HepG2  ENCODE Broad Chromatin State Segmentation by HMM (in HepG2 cells)    Schema   2011-01-21 
 HUVEC  ENCODE Broad Chromatin State Segmentation by HMM (in HUVEC cells)    Schema   2011-01-21 
 HMEC  ENCODE Broad Chromatin State Segmentation by HMM (in HMEC cells)    Schema   2011-01-21 
 HSMM  ENCODE Broad Chromatin State Segmentation by HMM (in HSMM cells)    Schema   2011-01-21 
 NHEK  ENCODE Broad Chromatin State Segmentation by HMM (in NHEK cells)    Schema   2011-01-21 
 NHLF  ENCODE Broad Chromatin State Segmentation by HMM (in NHLF cells)    Schema   2011-01-21 
     Restriction Policy
Source data version: through the ENCODE Jan 2011 Freeze


This track displays a chromatin state segmentation for each of nine human cell types. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements.

Display Conventions and Configuration

This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different cell type and displays individually on the browser. Instructions for configuring tracks with multiple subtracks are here. The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows:

  • State 1 -  Bright Red  - Active Promoter
  • State 2 -  Light Red  -Weak Promoter
  • State 3 -  Purple  - Inactive/poised Promoter
  • State 4 -  Orange  - Strong enhancer
  • State 5 -  Orange  - Strong enhancer
  • State 6 -  Yellow  - Weak/poised enhancer
  • State 7 -  Yellow  - Weak/poised enhancer
  • State 8 -  Blue  - Insulator
  • State 9 -  Dark Green  - Transcriptional transition
  • State 10 -  Dark Green  - Transcriptional elongation
  • State 11 -  Light Green  - Weak transcribed
  • State 12 -  Gray  - Polycomb-repressed
  • State 13 -  Light Gray  - Heterochromatin; low signal
  • State 14 -  Light Gray  - Repetitive/Copy Number Variation
  • State 15 -  Light Gray  - Repetitive/Copy Number Variation


ChIP-seq data from the Broad Histone track was used to generate this track. Data for nine factors plus input and nine cell types was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted).

Release Notes

This is release 1 (Jun 2011) of this track, and it is based on the NCBI36/hg18 release of the Broad Histone track. This track has also been lifted over to GRCh37/hg19. It is anticipated that the HMM methods will be run on the newer GRCh37/hg19 Broad Histone data and will replace the lifted version.


The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School, and the chromatin state segmentation was produced in Manolis Kellis's Computational Biology group at the Massachusetts Institute of Technology. Contact: Jason Ernst.

Data generation and analysis was supported by funds from the NHGRI (ENCODE), the Burroughs Wellcome Fund, Howard Hughes Medical Institute, NSF, Sloan Foundation, Massachusetts General Hospital and the Broad Institute.


Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.

There is no restriction on the use of segmentation data.