Annotation type

2987target gene predictions
1659candidate regulatory elements
1212accessible chromatin
969histone modifications
911chromatin state
796binding sites
648gene expression
466differential activity
174eQTL
126variant allelic effects
65Fine-mapped variants
22caQTL
7sQTL
5hQTL
4variant to gene
3meQTL
3other
3pQTL
1representative DNase hypersensitivity sites

Annotation Category

5548cis-regulatory elements
2987Target gene links
1114Gene expression levels
410Genetic variant effects
2Others

Annotation type Category

5112ChIP-seq
4418DNase-seq
520RNA-seq
496ATAC-seq
448snATAC-seq
270single cell RNA-seq
187HiC
142scRNA-seq
136H3K27ac ChIP-Seq
82snDropSeq
46pCHi-C
23snRNA-seq
17Expression arrays
5Capture-C
4RNA microarray
3DNA methylation profiling by array assay
3quantitative proteomics
1SNP-SELEX

Available data

7902bed bed3+
853tsv
837bed bed9
515bigWig
108txt
34bed bed9+
32bigBed bed9
26csv
16bigBed narrowPeak
12bed bed3
12bed narrowPeak
4bam
3bed gappedPeak
3xls

File set status

10059released
1archived
1revoked

Genome assembly (visualization)

6798hg19
3818GRCh38
4hg18

Organism

10013Homo sapiens

Biosample type

3764primary cell
3231tissue
2548cell line
512in vitro differentiated cells
4stem cell

Biosample term

135monocyte
110heart
107stomach
95kidney
93fibroblast
91endothelial cell
89brain
86head of caudate nucleus
84muscle of arm
82lung
82placenta
77adrenal gland
76A549
76small intestine
74macrophage
73CD8-positive, alpha-beta T cell
71muscle of leg
70large intestine
70smooth muscle cell
69muscle of back
68HeLa-S3
68T-cell
67left lung
66B cell
66common myeloid progenitor, CD34-positive
64CD4-positive, alpha-beta T cell
59dorsolateral prefrontal cortex
57thymus
56right lung
55hematopoietic multipotent progenitor cell
55stimulated activated CD4-positive, alpha-beta T cell
54H1-hESC
52hepatocyte
52neural progenitor cell
52right kidney
51natural killer cell
51renal cortex interstitium
50liver
50renal pelvis
48K562
48posterior cingulate gyrus
46adipocyte
45T cell
45islet of Langerhans
45left kidney
44heart left ventricle
43retina
41spinal cord
39CD14-positive monocyte
39spleen
38cardiac muscle cell
37CD4-positive, alpha-beta memory T cell
34pericyte
33MCF-7
33activated CD4-positive, alpha-beta T cell
33keratinocyte
32T-helper 1 cell
32glutamatergic neuron
31adipose tissue
31astrocyte
31pancreatic ductal cell
29heart right ventricle
29ovary
28T-helper 17 cell
28body of pancreas
28pancreas
28regulatory T cell
28tibial nerve
28trophoblast cell
27naive thymus-derived CD4-positive, alpha-beta T cell
26CD8-positive, alpha-beta memory T cell
26T-helper 2 cell
26epithelial cell of proximal tubule
25psoas muscle
25stimulated activated CD8-positive, alpha-beta memory T cell
24dendritic cell
24foreskin keratinocyte
24gastrocnemius medialis
24neuron
24pericyte cell
24sigmoid colon
23EndoC_BH1
23H9
23caudate nucleus
23foreskin fibroblast
23upper lobe of left lung
22GABAergic neuron
22HCT116
22glomerular endothelial cell
22thyroid gland
21right atrium auricular region
21testis
20breast cancer cell
20endothelial cell of lymphatic vessel
20mesenchymal stem cell
20mononuclear cell
20naive thymus-derived CD8-positive, alpha-beta T cell
20subcutaneous adipose tissue
20transverse colon
19HFFc6
19HepG2
19endocardial cell
19hepatic stellate cell
19omental fat pad
18embryonic stem cell
18mast cell
18muscle of trunk
18pancreatic beta cell
18pigmented layer of retina
17Peyer's patch
17erythroblast
17fibroblast of lung
17frontal cortex
16GM12878
16cerebellum
16chorionic villus
16fibroblast of cardiac tissue
16induced pluripotent stem cell
16layer of hippocampus
16left renal cortex interstitium
16skeletal muscle satellite cell
16substantia nigra
15activated T-cell
15bronchial epithelial cell
15mammary epithelial cell
15mammary gland epithelial cell
15pancreatic acinar cell
15pancreatic alpha cell
15pancreatic delta cell
15retinal pigment epithelial cell
15skeletal muscle myoblast
14activated CD8-positive, alpha-beta memory T cell
14endocrine pancreas
14left renal pelvis
14osteoblast
14right renal pelvis
14skeletal muscle tissue
13breast epithelium
13excitatory neuron
13fibroblast of dermis
13glomerular visceral epithelial cell
13left cardiac atrium
13naive B cell
13prostate gland
12Ammon's horn
12SK-N-DZ
12colonic mucosa
12epithelial cell of prostate
12lymphoblastoid cell line
11IMR-90
11SK-N-SH
11esophagus muscularis mucosa
11kidney tubule cell
11neuronal stem cell
11neurosphere
11neutrophil
11progenitor cell of endocrine pancreas
11putamen
10Rhabdomyosarcoma
10endodermal cell
10esophagus squamous epithelium
10foreskin melanocyte
10gastric cancer cell
10inflammatory macrophage
10limb
10lymphocyte
10neuroblastoma cell
10thyroid follicular cell
922Rv1
9GM06990
9HAP-1
9HT-29
9PC-9
9SK-N-MC
9WERI-Rb-1
9WI38
9cardiomyocytes
9diffuse intrinsic pontine glioma
9esophagus
9eye
9globus pallidus
9liposarcoma
9lower leg skin
9progenitor cell
9temporal lobe
9tongue
8B Cell
8GM12864
8GM12865
8HEK293
8LNCaP clone FGC
8MM.1S
8NAMALWA cell
8OCI-LY7
8T47D
8cingulate gyrus
8colon epithelial cell
8duodenal mucosa
8epithelial cell of esophagus
8fibroblast cell line

Organ

3365blood
vasculature
2861blood vessel
2853bodily fluid
2659vein
952epithelium
903brain
756kidney
518connective tissue
488heart
440lung
386musculature of body
358intestine
319pancreas
296skin of body
244limb
240liver
226large intestine
215embryo
174extraembryonic component
161eye
142adipose tissue
140stomach
111muscle organ
106bone element
104mammary gland
102adrenal gland
97placenta
97small intestine
93thymus
93uterus
88artery
87prostate gland
73ureter
64gonad
64penis
63spleen
62lymph node
60__MARKER__
49spinal cord
48esophagus
47thyroid gland
32ovary
31testis
25nerve
24lymphoid tissue
24skeleton
21lymphatic vessel
21mouth
16bronchus
15breast
13bone marrow
13pituitary gland
13urinary bladder
12tongue
12vagina
5trachea
4nose
1embryonic structure
1gallbladder
1pericardium

Life stage

2310adult
1381embryonic
454fetal
426unknown
115child
64newborn
32young adult
24postnatal

Date released

2541February, 2021
2436September, 2022
1984July, 2026
386May, 2021
357February, 2024
327November, 2021
320May, 2026
283June, 2020
251September, 2023
140May, 2020
127August, 2021
116March, 2020
103January, 2022
97October, 2022
73January, 2020
66March, 2023
59February, 2020
56January, 2021
49May, 2022
44November, 2022
40May, 2024
34August, 2017
33July, 2025
29March, 2024
28February, 2023
16April, 2020
12October, 2019
11November, 2019
9August, 2018
8April, 2019
8May, 2019
3November, 2020
3September, 2018
2January, 2018
2January, 2025
2March, 2026
1August, 2020
1August, 2022
1February, 2025
1July, 2020
1June, 2021

Software used

2501macs
2303r
998chromhmm
812encode-ccres
246abc
136qTLtools
121deltasvm
103deseq2
34cicero
27chicago
26nospecificsoft_customcode
25seurat
21gtex_eqtl:V8
21gtex_finemapping_eQTL:caveman
21gtex_finemapping_eQTL:caviar
21gtex_finemapping_eQTL:dapg
18samtools
15limix
14matrix-eQTL
12deeptools
12hiccups
12umitools
8fastqtl
8rasqual
6eigenmt
5peer
5salmon
5unknown
3mach2qtl
3minfi
3sqtlseeker
2combined S2G strategy
2emmax
2mpraflow
1altius-index
1bedops
1betacells_cytokines_t1d
1bimbam
1cisgenome
1e-range
1epacts
1fast-lmm
1haploview
1pepatac
1probabel
1snap
1spp

Encyclopedia version

1Adipocyte.narrowpeak.bed.gz Adipocyte.consensus_summit_features.bed.gz
1Endothelial.narrowpeak.bed.gz Endothelial.consensus_summit_features.bed.gz
1FAP.narrowpeak.bed.gz Mesenchymal_Stem_Cell.consensus_summit_features.bed.gz
1Macrophage.narrowpeak.bed.gz Macrophage.consensus_summit_features.bed.gz
1Neuromuscular_junction.narrowpeak.bed.gz Neuromuscular_junction.consensus_summit_features.bed.gz
1Neuronal.narrowpeak.bed.gz Neuronal.consensus_summit_features.bed.gz
1Satellite_Cell.narrowpeak.bed.gz Satellite_Cell.consensus_summit_features.bed.gz
1Smooth_Muscle.narrowpeak.bed.gz Smooth_Muscle.consensus_summit_features.bed.gz
1T_cell.narrowpeak.bed.gz T_cell.consensus_summit_features.bed.gz
1Type_1.narrowpeak.bed.gz Type_1.consensus_summit_features.bed.gz
1Type_2a.narrowpeak.bed.gz Type_2a.consensus_summit_features.bed.gz
1Type_2x.narrowpeak.bed.gz Type_2x.consensus_summit_features.bed.gz

Lab

8580AMP-T2D consortium
498Kyle Gaulton, UCSD
385Bing Ren, UCSD
246KPMP
136Jesse Engreitz, Stanford University
97Stephen Parker, UMich
53Katalin Susztak, Upenn
16Xin Sun, UCSD
10Ines Cebola, Imperial College London
9Anna Gloyn, Oxford
8Struan F.A. Grant, CHOP
5ITG
5Patrick T. Ellinor, Broad
4Doug Phanstiel, UNC
4Karen Mohlke, UNC
3Stephen S. Rich Lab @UVA
2Joseph Wu, Stanford

Project

9392AMP
327ENCODE
246KPMP
60T1D
16LungMap
15community
5ITG

Collection Tags

2427EpiMap
1824ChIP-Atlas
1458ENCODE-rE2G
932ENCODE
608DGA
524AMP
418T1D
400T2DKP
393HDMA
320pyxis
246KPMP
219BLUEPRINT
174 T2DKP
1744DN
135GTEx
133CATlas
108T2D
98eQTLCatalogue
96CMDGA
63HPAP
26FNIH_projects-heart
12FNIH_projects-liver
12ROADMAP

RFA