EnhancerAtlas 2.0: an updated resource with typical enhancer annotation in 600 tissue/cell types across nine species

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EnhancerAtlas 2.0 provides the downloading of tissue/cell specific enhancers in all 586 tissue/cell types across nine species. Based on the enhancer consensus and gene expression data, we predicted the target genes of enhancers for many tissue/cell types in human and mouse. Finally, the information of all individual datasets in each tissue/cell type was also attached here.

Download enhancers:


※Readme for the data format in the files

Enhancer matrix of all species by CSV format Enhancers of all species by bed format Enhancer matrix of all species by R object

Homo sapiens:
786-O A375 A549 Adipocyte AML_blast
Astrocyte BE2C BJ Bronchia_epithelial B_cell_blood
C4-2 Caco-2 Calu-3 CCRF-CEM CD133+
CD14+ CD14+_monocyte CD19+ CD20+ CD34+
CD36+ CD4+ CD8+ Cerebellum CMK
CNCC Colo320 Colo829 CUTLL1 CyT49
Denditric_cell DLD1 DOHH2 ECC-1 Endometrial_stromal_cell
endometrioid_adenocarcinoma ESC ESC_neuron ESC_NPC Esophagus
EWS502 Fetal_brain Fetal_heart Fetal_kidney Fetal_lung
Fetal_muscle_leg Fetal_placenta Fetal_small_intestine Fetal_spinal_cord Fetal_stomach
Fetal_thymus Fibroblast_foreskin Foreskin_keratinocyte FT246 FT33
GC_B_cell Gliobla GM10847 GM12878 GM12891
GM12892 GM18486 GM18505 GM18507 GM18508
GM18516 GM18522 GM18526 GM18951 GM19099
GM19141 GM19193 GM19238 GM19239 GM19240
H1 H128 H2171 H54 H9
HACAT HCASMC HCC1954 HCT116 Heart
HEK293 HEK293T HeLa-S3 Hela Hepatocyte
HepG2 HFF HL-60 hMADS-3 HMEC
hNCC HSC HSMM HSMMtube HT1080
HT29 HuCCT1 HUES64 HUVEC IMR90
iPSC Jurkat K562 Kasumi-1 KATO3
KB KELLY Keratinocyte Kidney Kidney_cortex
Left_ventricle LHCN-M2 Liver LNCaP-1F5 LNCaP-abl
LNCaP LoVo LP-1 LS174T Lung
LY1 Macrophage MCF-7 MCF10A MDA-MB-231
ME-1 Melanocyte melanoma Mesendoderm MM1S
Monocyte MS1 MSC_BM Myotube Namalwa
NB4 NCCIT NGP NH-A NHBE
NHDF NHEK NHLF NKC NT2-D1
OCI-LY1 OCI-Ly7 Osteobl Osteoblast Ovary
P493-6 PANC-1 Pancreas Pancreatic_islet PBMC
PC3 Plasma_cell_myeloma PrEC Raji Ramos
REH Retina RPE RPTEC RS4-11
SEM SGBS_adipocyte SH-SY5Y SK-MEL-5 SK-N-MC
SK-N-SH SK-N-SH_RA Skeletal_muscle SkMC Small_intestine
Sperm Spleen T47D-MTVL T47D T98G
TC-797 Th1 Th2 Thymus Treg_cell
Trophoblast U2OS U87 Urothelial_cell VCaP
ZR75-1 ZR75-30

Mus musculus:
3134 3T3-L1 416B Astrocyte AtT-20
B220+ BAT Bone_marrow Brain Brain_E14.5
Brown_preadipocyte_E18.5 B_cell B_cell_BM B_cell_lymph_node B_cell_spleen
C10 C3H10Thalf Cardiomyocyte CD172+DC CD19+
CD24+DC CD4+ CD4+CD8+ CD4+Treg CD4-CD8-
CD43- CD8+ Cerebellum Cerebellum_neonate CH12
CMP Cortex Cortex_embryo Dendritic_cell DR_cell
E14 Embryoid_body_cell Embryo_body Epididymis EpiLC
EpiSC Erythroblast_fetal_liver Erythroid_fetal_liver Erythroid_spleen ESC_46C
ESC_Bruce4 ESC_C6 ESC_D0 ESC_D3 ESC_hemangioblast
ESC_hematopoietic_progenitor ESC_hemogenic_endothelium ESC_J1 ESC_KH2 ESC_NPC
ESC_R ESC_R1 Fibroblast Forebrain_E11.5 Forebrain_E12.5
Forelimb_bud_embryo Forelimb_E11 Forelimb_E13 G1E-ER4 G1E
Gastrocnemius_muscle_myoblast Germline_stem_cell GMP Heart Heart_E11.5
Heart_E12.5 Heart_E14.5 Heart_neonate Hepatocyte HFSC
Hindbrain_E11.5 Hindlimb_bud_E11.5 HL-1 HPC7 HSC_BM
Intestine Intestine_crypt_progenitor Intestine_embryo IPSC Kidney
Kidney_embryo Kidney_neonate Large_intestine_epithelial Lens_P1 Limb_E11.5
Limb_E14.5 Liver_E14.5 Liver_neonate Liver_tumor LSK
Lung Lung_E14.5 Lung_neonate Lung_tumor Macrophage
Mammary_gland MC3T3-E1 MEF_E13.5 Megakaryocyte MEL
Mesodermal_cell Microglia Midbrain_E11 MoDC_BM MPP
MSC Myeloid_cell Neural_tube_embryo Neuron Neuron_cortical
Neuron_cortical_E16 Neuron_striatal NIH-3T3 NKC_spleen NKT
NPC NSC Nucleus_accumben Olfactory_bulb Olfactory_epithelium
Pancreas Pancreas_embryo Pancreatic_islet PCT4961 PDC
PDC_BM Peritoneal_macrophage Placenta Pre-B Pre-pro-B
Pro-B_BM Prostate Retina_neonate Rib_chondrocyte_P1 Sperm
Spermatid Spleen Spleen_leukemia Stomach_neonate Striatum
Testis Th1 Th2 Thymocyte Thymus
Treg_cell TSC Uterus V6.5 WAT
ZHBTc4

Drosophila melanogaster:
Adult_fly_brain BG3-c2 Blastoderm embryo_1-3 embryo_16-20
embryo_2-3 embryo_2-4 embryo_5-13 embryo_6-8 Embryo_muscle
embryo_NC14 Kc167 L3_brain L3_eye_ante_discs L3_eye_discs
L3_wing_disc Neuron OSC Ovary Pupae
S2

Caenorhabditis elegans:
Embryo Embryo_early Embryo_late Embryo_mixed Larvae_L1
Larvae_L2 Larvae_L3 Larvae_L4 Young_adult

Danio rerio:
Embryo_2.5hpf Embryo_24hpf Embryo_36hpf Embryo_4.5hpf Embryo_48hpf
Embryo_4hpf Embryo_5-6ss Embryo_72hpf Embryo_bud Embryo_dome
Embryo_epiboly_80 Embryo_sphere Intestine Melanoma Red_blood_cell

Rattus norvegicus:
Chondrosarcoma GC_pituitary_cell INS-1E Liver Neuron
NRVM Oligodendrocyte Oligodendrocyte_precursor RASMC Schwann_cell
Sciatic_nerve

Gallus gallus:
DT40 Embryo_skin limb_bud_MC_E4.5

Sus scrofa:
Heart iPSC

Saccharomyces cerevisiae:
Asynchronous_cell     Log_cell Phase_G1 Phase_S Phase_S_early
Quiescent_cell Yeast_cell

SNPs with enhancers:


786-O A375 A549 Adipocyte AML_blast
Astrocyte BE2C BJ Bronchia_epithelial B_cell_blood
C4-2 Caco-2 Calu-3 CCRF-CEM CD133+
CD14+ CD14+_monocyte CD19+ CD20+ CD34+
CD36+ CD4+ CD8+ Cerebellum CMK
CNCC Colo320 Colo829 CUTLL1 CyT49
Denditric_cell DLD1 DOHH2 ECC-1 Endometrial_stromal_cell
endometrioid_adenocarcinoma ESC ESC_neuron ESC_NPC Esophagus
EWS502 Fetal_brain Fetal_heart Fetal_kidney Fetal_lung
Fetal_muscle_leg Fetal_placenta Fetal_small_intestine Fetal_spinal_cord Fetal_stomach
Fetal_thymus Fibroblast_foreskin Foreskin_keratinocyte FT246 FT33
GC_B_cell Gliobla GM10847 GM12878 GM12891
GM12892 GM18486 GM18505 GM18507 GM18508
GM18516 GM18522 GM18526 GM18951 GM19099
GM19141 GM19193 GM19238 GM19239 GM19240
H1 H128 H2171 H54 H9
HACAT HCASMC HCC1954 HCT116 Heart
HEK293 HEK293T HeLa-S3 Hela Hepatocyte
HepG2 HFF HL-60 hMADS-3 HMEC
hNCC HSC HSMM HSMMtube HT1080
HT29 HuCCT1 HUES64 HUVEC IMR90
iPSC Jurkat K562 Kasumi-1 KATO3
KB KELLY Keratinocyte Kidney Kidney_cortex
Left_ventricle LHCN-M2 Liver LNCaP-1F5 LNCaP-abl
LNCaP LoVo LP-1 LS174T Lung
LY1 Macrophage MCF-7 MCF10A MDA-MB-231
ME-1 Melanocyte melanoma Mesendoderm MM1S
Monocyte MS1 MSC_BM Myotube Namalwa
NB4 NCCIT NGP NH-A NHBE
NHDF NHEK NHLF NKC NT2-D1
OCI-LY1 OCI-Ly7 Osteobl Osteoblast Ovary
P493-6 PANC-1 Pancreas Pancreatic_islet PBMC
PC3 Plasma_cell_myeloma PrEC Raji Ramos
REH Retina RPE RPTEC RS4-11
SEM SGBS_adipocyte SH-SY5Y SK-MEL-5 SK-N-MC
SK-N-SH SK-N-SH_RA Skeletal_muscle SkMC Small_intestine
Sperm Spleen T47D-MTVL T47D T98G
TC-797 Th1 Th2 Thymus Treg_cell
Trophoblast U2OS U87 Urothelial_cell VCaP
ZR75-1 ZR75-30

Download enhancer-gene interactions:


Homo sapiens
A375 A549 AML_blast Astrocyte BJ Bronchia_epithelial
Caco-2 Calu-3 CD14+ CD19+ CD20+ CD34+
CD36+ CD4+ CD8+ Cerebellum CUTLL1 DOHH2
ECC-1 ESC_neuron Esophagus Fetal_heart Fetal_kidney Fetal_muscle_leg
Fetal_placenta Fetal_small_intestine Fetal_spinal_cord Fetal_stomach Fetal_thymus FT246
FT33 GM10847 GM12878 GM12891 GM12892 GM18505
GM18526 GM18951 GM19099 GM19193 GM19238 GM19239
GM19240 H1 H9 HCC1954 HCT116 HEK293T
HEK293 Hela-S3 Hela HepG2 HFF HL-60
hMADS-3 HMEC hNCC HSMM HT1080 HT29
HUVEC IMR90 Jurkat K562 Kasumi-1 KB
Keratinocyte Left_ventricle LHCN-M2 Liver LNCaP-abl LNCaP
Lung MCF-7 MCF10A ME-1 Melanocyte melanoma
Mesendoderm MS1 Myotube Namalwa NB4 NHDF
NHEK NHLF NKC OCI-Ly7 Osteoblast Ovary
PANC-1 Pancreas Pancreatic_islet PBMC PC3 PrEC
SGBS_adipocyte SK-N-SH SK-N-SH_RA Skeletal_muscle Small_intestine Sperm
Spleen T47D T98G th1 Thymus U2OS
VCaP ZR75-30

Mus musculus
3T3-L1 416B AtT-20 BAT Bone_marrow Brain_E14.5
Brown_preadipocyte_E18.5 C3H10Thalf CD19+ CD4+CD8+ CD4+Treg CD4+
CD8+ Cerebellum Cerebellum_neonate CH12 CMP Cortex
Dendritic_cell EpiLC EpiSC Erythroid_fetal_liver Erythroid_spleen ESC_Bruce4
ESC_J1 ESC_KH2 ESC_NPC Forebrain_E11.5 Forebrain_E12.5 Forelimb_bud_embryo
Forelimb_E11 Forelimb_E13 G1E-ER4 G1E GMP Heart_E11.5
Heart_E12.5 Heart_E14.5 Heart Hepatocyte HFSC Hindbrain_E11.5
Intestine IPSC Kidney Large_intestine_epithelial Lens_P1 Limb_E11.5
Limb_E14.5 Liver_E14.5 Liver Lung_E14.5 Lung Lung_neonate
MC3T3-E1 Megakaryocyte MEL Microglia Midbrain_E11 Neuron_cortical
NIH-3T3 NKC_spleen NKT NPC Olfactory_bulb Pancreas
Pancreatic_islet PDC_BM PDC Peritoneal_macrophage Placenta Pre-B
Pre-pro-B Pro-B_BM Prostate Rib_chondrocyte_P1 Spermatid Spleen
Stomach_neonate Striatum Testis Th1 Th2 Thymus
Treg_cell Uterus V6.5 WAT ZHBTc4

Drosophila melanogaster
BG3-c2 Kc167 L3_brain L3_eye_ante_discs L3_wing_disc
OSC S2

※Data format in the file

Data source:


Homo sapiens:
MSC_BM RS4-11 H2171 Pancreatic_islet HL-60
GM18505 HUVEC Hepatocyte FT246 HCC1954
MDA-MB-231 PANC-1 NGP Endometrial_stromal_cell Calu-3
HFF Plasma_cell_myeloma Caco-2 HEK293T Th2
Gliobla GM12892 SK-N-MC SEM MM1.S
MS1 Retina Th1 OCI-LY1 ESC_neuron
HT1080 KELLY HSMMtube Adipocyte ZR75-1
ZR75-30 ECC-1 REH SK-N-SH_RA Cerebellum
Monocyte PrEC SK-N-SH SkMC Osteobl
GM19193 H9 Raji T98G KB
CD14+_monocyte GM18507 Jurkat GM19239 CCRF-CEM
Spleen Fetal_stomach Urothelial_cell NT2-D1 CNCC
Fibroblast H128 Kidney RPTEC Fetal_kidney
CUTLL1 H54 Mesendoderm LS174T Keratinocyte
HeLa-S3 HACAT endometrioid_adenocarcinoma LP-1 ESC_NPC
Denditric_cell U87 Small_intestine C4-2 GM12891
Fetal_lung FT33 Pancreas ESC PC3
CyT49 HMEC SGBS_adipocyte MCF10A Colo320
HT29 LCL H1 Heart T47D-MTVL
hMADS-3 GM18526 Namalwa MV4-11 Kasumi-1
Melanocyte LHCN-M2 melanoma RPE NKC
K562 SK-MEL-5 GM10847 DU145 LNCaP-abl
T47D Thymus Kidney_cortex Sperm NHBE
CD14+ Fetal_brain iPSC MSC LNCaP-1F5
BE2C GM19099 NCCIT CMK Trophoblast
B_cell_blood DOHH2 Colo829 HuCCT1 GM19141
ME-1 CD8+ HUES64 LY1 Liver
hNCC Treg_cell Ramos LNCaP GM19238
KATO3 NHEK HCASMC NB4 GC_B_cell
CD36+ GM12878 786-O CD19+ Macrophage
HSC NHLF BJ SH-SY5Y PBMC
TC-797 Fetal_heart DLD1 P493-6 A375
AML_blast OCI-Ly7 EWS502 GM19240

Mus musculus:
Hepatocyte 3T3-L1 GMP BAT EpiLC
MEL Pro-B_BM Kidney RAW_macrophage Cortex_embryo
ESC_C6 PDC_BM TSC Forebrain_E12.5 Limb_E14.5
Hindlimb_bud_E11.5 Epididymis CD43- Thymocyte G1E-ER4
Fibroblast Treg_cell HFSC C10 416B
MEF_E13.5 HL-1 Germline_stem_cell B_cell_spleen NIH-3T3
Intestine_crypt_progenitor Olfactory_epithelium Brain ESC_KH2 Th1
Neuron_cortical_E16 Liver_tumor Forelimb_E13 CD8+ Macrophage
Myeloid_cell Pancreas Spleen_leukemia B_cell NKC_spleen
ESC_R1 Cortex BMDM Pre-B Striatum
Erythroid_fetal_liver Pancreas_embryo B_cell_BM LSK Olfactory_bulb
ZHBTc4 G1E Large_intestine_epithelial EpiSC IPSC
Testis CD4+ PDC Neuron_cortical Intestine_embryo
DR_cell Sperm ESC_hemogenic_endothelium CD172+DC B_cell_lymph_node
Retina_neonate Bone_marrow Placenta Peritoneal_macrophage AtT-20
Astrocyte Heart Pancreatic_islet NSC CD24+DC
Heart_E11.5 Cerebellum_neonate Mammary_gland Cerebellum ESC_R
Lung_E14.5 Spleen ESC_hematopoietic_progenitor Erythroblast_fetal_liver Kidney_embryo
Forelimb_bud_embryo Lung CMP ESC_46C Megakaryocyte
CD4+CD8+ Forelimb_E11 WAT Hindbrain_E11.5 Forebrain_E11.5
Mesodermal_cell Kidney_neonate Spermatid Liver_E14.5 PCT4961
Th2 ESC_hemangioblast V6.5 Neural_tube_embryo C3H10Thalf
CH12 Liver_neonate Gastrocnemius_muscle_myoblast Brown_preadipocyte_E18.5 Stomach_neonate
3134 Rib_chondrocyte_P1 Microglia Prostate ESC_NPC
CD4+Treg Heart_E14.5 ESC_D0 Erythroid_spleen HSC_BM
Neuron_striatal Embryo_body Midbrain_E11 Lung_tumor ESC_D3
ESC_Bruce4 Testis_neonate Nucleus_accumben NPC Pre-pro-B
Neuron Lung_neonate Heart_neonate CD19+ Uterus
Lens_P1 Embryoid_body_cell MSC Dendritic_cell HPC7
Intestine Thymus Cardiomyocyte Limb_E11.5 MC3T3-E1
B220+ Brain_E14.5 MPP MoDC_BM CD4-CD8-
ESC_J1 E14 Heart_E12.5 NKT

Drosophila melanogaster:
embryo_NC14 Adult_fly_brain embryo_1-3 L3_eye_discs S2
embryo_6-8 Embryo_muscle embryo_5-13 Neuron Pupae
Ovary embryo_2-3 embryo_2-4 Kc167 L3_wing_disc
L3_eye_ante_discs L3_brain OSC embryo_16-20 Blastoderm
BG3-c2

Caenorhabditis elegans:
Young_adult Larvae_L1 Embryo Larvae_L2 Embryo_mixed
Embryo_early Larvae_L3 Larvae_L4 Embryo_late

Danio rerio:
Embryo_48hpf Embryo_2.5hpf Intestine Embryo_epiboly_80 Embryo_dome
Embryo_72hpf Embryo_sphere Red_blood_cell Embryo_5-6ss Embryo_bud
Embryo_4hpf Embryo_36hpf Embryo_24hpf Embryo_4.5hpf Melanoma

Rattus norvegicus:
Neuron Oligodendrocyte_precursor Schwann_cell GC_pituitary_cell Sciatic_nerve
Oligodendrocyte Chondrosarcoma NRVM RASMC Liver
INS-1E

Gallus gallus:
DT40 limb_bud_MC_E4.5 Embryo_skin

Sus scrofa:
iPSC Heart

Saccharomyces cerevisiae:
Quiescent_cell Log_cell Phase_G1 Asynchronous_cell Phase_S
Phase_S_early Yeast_cell