ENCODE Regulation Chromatin State Track Settings
Chromatin state of embryonic tissue (12 tissues, 8 ages) from ENCODE 3 (UCSD/Ren)

Track collection:
Integrated Regulation from ENCODE

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E11.5   E11.5
E12.5   E12.5
E13.5   E13.5
E14.5   E14.5
E15.5   E15.5
E16.5   E16.5
P0   P0
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  Tissue↓1 Age↓2   Track Name↓3  
 forebrain  E11.5  Chromatin state of embryonic day E11.5 forebrain from ENCODE 3 (UCSD/Ren)   Schema 
 forebrain  E13.5  Chromatin state of embryonic day E13.5 forebrain from ENCODE 3 (UCSD/Ren)   Schema 
 forebrain  E15.5  Chromatin state of embryonic day E15.5 forebrain from ENCODE 3 (UCSD/Ren)   Schema 
 forebrain  P0  Chromatin state of day P0 forebrain from ENCODE 3 (UCSD/Ren)   Schema 
 heart  E11.5  Chromatin state of embryonic day E11.5 heart from ENCODE 3 (UCSD/Ren)   Schema 
 heart  E13.5  Chromatin state of embryonic day E13.5 heart from ENCODE 3 (UCSD/Ren)   Schema 
 heart  E15.5  Chromatin state of embryonic day E15.5 heart from ENCODE 3 (UCSD/Ren)   Schema 
 heart  P0  Chromatin state of day P0 heart from ENCODE 3 (UCSD/Ren)   Schema 


The ENCODE project has established an epigenomic resource for mammalian development, profiling a diverse panel of mouse tissues at eight developmental stages from 10.5 days post conception until birth.

This track set presents chromatin state annotations derived from ChIP-seq of histone modifications performed by the laboratory of Bing Ren as part of the ENCODE Consortium, phase 3.

The chromHMM method was used to integrate ChIP-seq data from 8 histone modifications (H3K27ac, H3K27me3, H3K4me3, H3K4me2, H3K4me1, H3K9me3, H3K9ac, H3K36me3). In total, fifteen chromatin states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements.

The histone ChIP-seq data underlying this track are presented in the Histone Modifications track.

Display Conventions and Configuration

This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different tissue and age, and displays individually on the browser.

The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows:

  • State 1 -       Dark Green - Promoter, Active (Pr-A)
  • State 2 -       Light Green - Promoter, Weak (Pr-W)
  • State 3 -       Light Grey - Promoter, Bivalent (Pr-B)
  • State 4 -       Green - Promoter, Flanking Region (Pr-F)
  • State 5 -       Bright Yellow - Enhancer, Strong TSS-distal (En-Sd)
  • State 6 -       Bright Yellow - Enhancer, Strong TSS-proximal (En-Sp)
  • State 7 -       Light Yellow - Enhancer, Weak (En-W)
  • State 8 -       Dark Grey - Enhancer, Poised TSS-distal (En-Pd)
  • State 9 -       Dark Grey - Enhancer, Poised TSS-proximal (En-Pp)
  • State 10 -       Dark Blue - Transcription, Strong (Tr-S)
  • State 11 -       Royal Blue - Transcription, Permissive (Tr-P)
  • State 12 -       Light Blue - Transcription, Initiation (Tr-I)
  • State 13 -       State 13 - Salmon - Heterochromatin, Polycomb-associated (Hc-P)
  • State 14 -       Pink - Heterochromatin, H3K9me3-associated (Hc-H)
  • State 15 -       White - No significant signal (Ns)

This track is configured by default to "pack" display mode with the state labels displayed. To display without labels, switch the track to "dense" display mode.


To leverage chromatin state information captured by patterns of histone modifications, ChromHMM analysis was applied to ChIP-seq data from 8 histone modifications, producing a 15-state model that shows high consistency between biological replicates and general agreement with previously published models. The states were then used to segment the genome in each tissue and stage.

Each state was assigned a descriptive label based on its genomic distribution and similarity to known chromatin signatures. The resulting chromatin states fall into 4 broad functional classes: promoter, enhancer, transcriptional, and heterochromatic.

This track set represents pooled chromatin state calls, in which ChIP-seq for two biological replicates that were was pooled prior to chromatin state segmentation.

Data Access

ChromHMM segmentation for individual and pooled replicates can be downloaded from the Ren Lab ENCODE3 mouse histone and ATAC-seq paper supplementary data page. The underlying ChIP-seq data are publicly available from the ENCODE portal, and can be directly accessed here.


Thanks to Iros Barozzi and colleagues in the Environmental Genomics and Systems Biology Division at the Lawrence Berkeley National Laboratory for generating the chromHmm analysis and to David Gorkin and Yanxiao Zhang at the Ren lab (UCSD/Ludwig Institute for Cancer Research) for providing these data and assisting with track development at UCSC.


Gorkin et al. An atlas of dynamic chromatin landscapes in the developing mouse fetus. Nature, In Press. (pre-print: doi: https://doi.org/10.1101/166652)

Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012 Feb 28;9(3):215-6. PMID: 22373907; PMC: PMC3577932

Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. PMID: 26527727; PMC: PMC4702836