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chromHMM tracks from Roadmap

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*Data Type*:	Real	Imputed

All	*views*	AuxiliaryHMM	PrimaryHMM	ImputedHMM
*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

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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

Roadmap Consortium project home page
NCBI Epigenomics Gateway portal to all project data in GEO database
Epigenome Data and Analysis Coordination Center/EDACC