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  Data Type: Real Imputed
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Sample Type
HepG2 
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells 
Lung 
Ovary 
Thymus 
HMEC 
CD4 Naive Primary cells 
CD4+ CD25- CD45RA+ Naive Primary Cells 
CD8 Naive Primary cells 
CD4 Memory Primary cells 
Mobilized CD34 Primary cells 
CD3 Primary cells 
Stomach Mucosa 
CD19 Primary cells 
Penis Foreskin Fibroblast Primary Cells 
Penis Foreskin Melanocyte Primary Cells 
H9 
HUES48 
HUES64 
H1 
hES-I3 
WA-7 
CD14 primary cells 
HUVEC 
Dnd41 
Adult Liver 
Bone Marrow Derived Mesenchymal Stem cell 
Adipose Nuclei 
Colonic Mucosa 
Rectal Mucosa 
CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells 
CD4+ CD25- CD45RO+ Memory Primary Cells 
CD8 Memory Primary Cells 
CD4+ CD25int CD127+ Tmem Primary Cells 
Brain Germinal Matrix 
H9 Derived Neuronal Progenitor Cultured Cells 
CD4+ CD25- Th Primary Cells 
Esophagus 
Right Atrium 
Brain Angular Gyrus 
Duodenum Smooth Muscle 
Duodenum Mucosa 
iPS DF 19.11 
iPS DF 6.9 
Breast vHMEC 
Breast Myoepithelial cells 
Rectal Smooth Muscle 
Skeletal Muscle 
Stomach Smooth Muscle 
Muscle Satellite Cultured Cells 
Peripheral Blood Mononuclear Primary cells 
hiPS-20b 
CD34 Primary cells 
CD15 Primary cells 
PanIslets 
hiPS-15b 
CD4+ CD25+ CD127- Treg Primary Cells 
Fetal Lung 
Fetal Kidney 
Monocytes-CD14+ 
hiPS-18b 
Fetal Placenta 
Fetal Intestine Small 
Fetal Muscle Trunk 
Fetal Muscle Leg 
HeLa-S3 
Fetal Adrenal Gland 
Fetal Intestine Large 
Fetal Thymus 
NH-A 
NHDF-Ad 
NHEK 
NHLF 
HSMM 
HSMMtube 
Psoas Muscle 
H1 Derived Neuronal Progenitor Cultured Cells 
Placenta Amnion 
Aorta 
Right Ventricle 
Gastric 
Osteobl 
Sigmoid Colon 
Left Ventricle 
Colon Smooth Muscle 
A549 
K562 
Brain Inferior Temporal Lobe 
Brain Hippocampus Middle 
Brain Cingulate Gyrus 
Brain Anterior Caudate 
GM12878 
Pancreas 
Brain Substantia Nigra 
Brain Mid Frontal Lobe 
Spleen 
Mesenchymal Stem Cell Derived Adipocyte Cultured Cells 
Small Intestine 
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells 
H1 BMP4 Derived Mesendoderm Cultured Cells 
IMR90 
H1 Derived Mesenchymal Stem Cells 
H1 BMP4 Derived Trophoblast Cultured Cells 
Adipose Derived Mesenchymal Stem Cell Cultured Cells 
HUES6 
UCSF-4star 
H9 Derived Neuron Cultured Cells 
Fetal Brain 
Fetal Heart 
CD34 cultured cells 
Fetal Stomach 
hESC Derived CD56+ Mesoderm Cultured Cells 
hESC Derived CD56+ Ectoderm Cultured Cells 
CD56 primary cells 
Penis Foreskin Keratinocyte Primary Cells 
Neurospheres, Cortex Derived 
Neurospheres, Ganglionic Eminence Derived 
hESC Derived CD184+ Endoderm Cultured Cells 
Sample Type
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 IMR90  AuxiliaryHMM  E017 IMR90 fetal lung fibroblasts Cell Line AuxiliaryHMM    Data format 
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 IMR90  PrimaryHMM  E017 IMR90 fetal lung fibroblasts Cell Line PrimaryHMM    Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Vizhub @ Wash U built this track, and Roadmap Epigenomics Consortium is responsible for its contents.

Description

This track displays a chromatin state segmentation for the cell types used by Roadmap Consortium. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for 5 core marks (H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9ac, H3K9me3) + H3K27ac using a Hidden Markov Model (HMM). In total, 15 states (Primary), 18 states (Auxiliary) and 25 states (Imputed) 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. The 18 states of the HMM, their associated segment color, and the candidate annotations are as follows:

Primary Core Marks segmentation

  • State 1 -  Red  - TssA (Active_TSS)
  • State 2 -  OrangeRed  - TssAFlnk (Flanking_Active_TSS)
  • State 3 -  LimeGreen  - TxFlnk (Transcr_at_gene_5_and_3primer)
  • State 4 -  Green  - Tx (Strong_transcription)
  • State 5 -  DarkGreen  - TxWk (Weak_transcription)
  • State 6 -  GreenYellow  - EnhG (Genic_enhancers)
  • State 7 -  Yellow  - Enh (Enhancers)
  • State 8 -  MediumAquamarine  - ZNF/Rpts (ZNF_genes&repeats)
  • State 9 -  PaleTurquoise  - Het (Heterochromatin)
  • State 10 -  IndianRed  - TssBiv (Bivalent/Poised_TSS)
  • State 11 -  DarkSalmon  - BivFlnk (Flanking_Bivalent_TSS/Enh)
  • State 12 -  DarkKhaki  - EnhBiv (Bivalent_Enhancer)
  • State 13 -  Silver  - ReprPC (Repressed_PolyComb)
  • State 14 -  Gainsboro  - ReprPCWk (Weak_Repressed_PolyComb)
  • State 15 -  White  - Quies (Quiescent/Low)

Auxiliary Core Marks + K27ac segmentation

  • State 1 -  Red  - TssA (Active_TSS)
  • State 2 -  Orange_Red  - TssFlnk (Flanking_TSS)
  • State 3 -  Orange_Red  - TssFlnkU (Flanking_TSS_Upstream)
  • State 4 -  Orange_Red  - TssFlnkD (Flanking_TSS_Downstream)
  • State 5 -  Green  - Tx (Strong_transcription)
  • State 6 -  DarkGreen  - TxWk (Weak_transcription)
  • State 7 -  GreenYellow  - EnhG1 (Genic_enhancer1)
  • State 8 -  GreenYellow  - EnhG2 (Genic_enhancer2)
  • State 9 -  Orange  - EnhA1 (Active_Enhancer1)
  • State 10 -  Orange  - EnhA2 (Active_Enhancer2)
  • State 11 -  Yellow  - EnhWk (Weak_Enhancer)
  • State 12 -  Medium_Aquamarine  - ZNF/Rpts (ZNF_genes&repeats)
  • State 13 -  PaleTurquoise  - Het (Heterochromatin)
  • State 14 -  IndianRed  - TssBiv (Bivalent/Poised_TSS)
  • State 15 -  DarkKhaki  - EnhBiv (Bivalent_Enhancer)
  • State 16 -  Silver  - ReprPC (Repressed_PolyComb)
  • State 17 -  Gainsboro  - ReprPCWk (Weak_Repressed_PolyComb)
  • State 18 -  White  - Quies (Quiescent/Low)

Imputed Marks Segmentation

  • State 1 -  Red  - TssA (Active TSS)
  • State 2 -  Orange Red  - PromU (Promoter Upstream TSS)
  • State 3 -  Orange Red  - PromD1 (Promoter Downstream TSS with DNase)
  • State 4 -  Orange Red  - PromD2 (Promoter Downstream TSS)
  • State 5 -  Green  - Tx5' (Transcription 5')
  • State 6 -  Green  - Tx (Transcription)
  • State 7 -  Green  - Tx3' (Transcription 3')
  • State 8 -  Light Green  - TxWk (Weak transcription)
  • State 9 -  GreenYellow  - TxReg (Transcription Regulatory)
  • State 10 -  GreenYellow  - TxEnh5' (Transcription 5' Enhancer)
  • State 11 -  GreenYellow  - TxEnh3' (Transcription 3' Enhancer)
  • State 12 -  GreenYellow  - TxEnhW (Transcription Weak Enhancer)
  • State 13 -  Orange  - EnhA1 (Active Enhancer 1)
  • State 14 -  Orange  - EnhA2 (Active Enhancer 2)
  • State 15 -  Orange  - EnhAF (Active Enhancer Flank)
  • State 16 -  Yellow  - EnhW1 (Weak Enhancer 1)
  • State 17 -  Yellow  - EnhW2 (Weak Enhancer 2)
  • State 18 -  Yellow  - EnhAc (Enhancer Acetylation Only)
  • State 19 -  Light Yellow  - DNase (DNase only)
  • State 20 -  Medium Aquamarine  - ZNF/Rpts (ZNF genes & repeats)
  • State 21 -  PaleTurquoise  - Het (Heterochromatin)
  • State 22 -  Light Purple  - PromP (Poised Promoter)
  • State 23 -  Purple  - PromBiv (Bivalent Promoter)
  • State 24 -  Silver  - ReprPC (Repressed PolyComb)
  • State 25 -  White  - Quies (Quiescent/Low)

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

Data were generated by Anshul Kundaje from the Roadmap Consortium.

Release Notes

The data is combination of Release II, III, IV, V, VI, VII, VIII and IX which were mapped to human reference genome version hg19. The data is production of Roadmap Epigenomics Project.

Please follow the link for Roadmap Epigenomics data access policy

Credits

These data were generated in labs from the Roadmap Epigenomics Project.

Useful links