Variant report

Variant	rs554391760
Chromosome Location	chr3:56590644-56590645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56590599-56591968	HepG2	liver:	n/a	n/a
2	MXI1	chr3:56590612-56592100	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:56590638-56591604	PFSK-1	brain:	n/a	n/a
4	MYC	chr3:56590487-56591972	K562	blood:	n/a	n/a
5	ZNF384	chr3:56590480-56590706	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:56590356-56592659	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:56590499-56592047	K562	blood:	n/a	n/a
8	E2F4	chr3:56590491-56590722	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr3:56590609-56591814	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:56590569-56592147	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr3:56590484-56592278	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:56590605-56591426	GM12878	blood:	n/a	n/a
13	IRF1	chr3:56590586-56591945	K562	blood:	n/a	chr3:56591554-56591563
14	TBP	chr3:56590528-56592139	K562	blood:	n/a	n/a
15	POLR2A	chr3:56590640-56591480	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:56590590-56592032	K562	blood:	n/a	n/a
17	CEBPB	chr3:56590587-56591851	K562	blood:	n/a	chr3:56591677-56591694
18	HCFC1	chr3:56590644-56592693	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:56590593-56591898	K562	blood:	n/a	n/a
20	TEAD4	chr3:56590462-56591341	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr3:56590599-56591610	HCT-116	colon:	n/a	n/a
22	POLR2A	chr3:56590629-56591578	ProgFib	skin:	n/a	n/a
23	ZNF384	chr3:56590354-56590729	K562	blood:	n/a	n/a
24	TBP	chr3:56590639-56592033	H1-hESC	embryonic stem cell:	n/a	n/a
25	TEAD4	chr3:56590507-56591229	H1-hESC	embryonic stem cell:	n/a	n/a
26	REST	chr3:56590444-56592120	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr3:56590174-56592533	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr3:56588808..56592620-chr3:56662133..56663692,3	K562	blood:
3	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
4	chr17:61042877..61045351-chr3:56589650..56591304,2	MCF-7	breast:
5	chr3:56589716..56592620-chr3:56662133..56663652,2	K562	blood:

No data

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000263931	Chromatin interaction
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3417076	chr3:56590062-56591960	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56590000-56592000	Active TSS	NHDF-Ad	bronchial
2	chr3:56590200-56591800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:56590200-56592000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:56590200-56592000	Active TSS	Duodenum Mucosa	Duodenum
5	chr3:56590200-56592000	Active TSS	Fetal Heart	heart
6	chr3:56590200-56592000	Active TSS	Fetal Kidney	kidney
7	chr3:56590200-56592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:56590200-56592600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:56590200-56592600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:56590200-56592600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:56590400-56590800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:56590400-56590800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr3:56590400-56590800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr3:56590400-56590800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:56590400-56590800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:56590400-56590800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:56590400-56590800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:56590400-56591200	Active TSS	Primary hematopoietic stem cells	blood
19	chr3:56590400-56591200	Active TSS	HepG2	liver
20	chr3:56590400-56591400	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr3:56590400-56591400	Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr3:56590400-56591400	Active TSS	Adipose Nuclei	Adipose
23	chr3:56590400-56591800	Active TSS	Primary monocytes fromperipheralblood	blood
24	chr3:56590400-56591800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:56590400-56591800	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr3:56590400-56591800	Active TSS	Liver	Liver
27	chr3:56590400-56591800	Active TSS	Brain Substantia Nigra	brain
28	chr3:56590400-56591800	Active TSS	Colon Smooth Muscle	Colon
29	chr3:56590400-56591800	Active TSS	Fetal Brain Male	brain
30	chr3:56590400-56591800	Active TSS	Fetal Lung	lung
31	chr3:56590400-56591800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:56590400-56591800	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:56590400-56591800	Active TSS	HSMMtube	muscle
34	chr3:56590400-56592000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:56590400-56592000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:56590400-56592000	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr3:56590400-56592000	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr3:56590400-56592000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr3:56590400-56592000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr3:56590400-56592000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:56590400-56592000	Active TSS	Brain Anterior Caudate	brain
42	chr3:56590400-56592000	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:56590400-56592000	Active TSS	Brain Hippocampus Middle	brain
44	chr3:56590400-56592000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:56590400-56592000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr3:56590400-56592000	Active TSS	Fetal Muscle Leg	muscle
47	chr3:56590400-56592000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:56590400-56592000	Active TSS	Psoas Muscle	Psoas
49	chr3:56590400-56592000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:56590400-56592000	Active TSS	Skeletal Muscle Female	skeletal muscle

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