Variant report

Variant	rs563611939
Chromosome Location	chr2:86565047-86565048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:86563461-86565056	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr2:86564857-86565049	Hela-S3	cervix:	n/a	n/a
3	HA-E2F1	chr2:86564164-86565140	Hela-S3	cervix:	n/a	chr2:86564789-86564799 chr2:86564390-86564400 chr2:86564964-86564971 chr2:86564962-86564972 chr2:86564391-86564401 chr2:86564963-86564971 chr2:86564394-86564404 chr2:86564733-86564743 chr2:86564756-86564765 chr2:86564963-86564971
4	HA-E2F1	chr2:86564787-86565392	MCF-7	breast:	n/a	chr2:86564789-86564799 chr2:86564964-86564971 chr2:86564962-86564972 chr2:86564963-86564971 chr2:86564963-86564971
5	E2F1	chr2:86564184-86565170	Hela-S3	cervix:	n/a	chr2:86564789-86564799 chr2:86564390-86564400 chr2:86564964-86564971 chr2:86564962-86564972 chr2:86564391-86564401 chr2:86564963-86564971 chr2:86564394-86564404 chr2:86564733-86564743 chr2:86564770-86564785 chr2:86564756-86564765 chr2:86564963-86564971
6	POLR2A	chr2:86563062-86565332	H1-neurons	neurons:	n/a	n/a
7	SIN3A	chr2:86563706-86565367	H1-hESC	embryonic stem cell:	n/a	chr2:86564364-86564377 chr2:86565008-86565017
8	MAZ	chr2:86564849-86565079	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:86563464-86565221	H1-neurons	neurons:	n/a	n/a
10	MAFK	chr2:86565043-86565170	Hela-S3	cervix:	n/a	n/a
11	CTBP2	chr2:86564814-86565257	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr2:86562875-86565396	H1-neurons	neurons:	n/a	chr2:86565007-86565017 chr2:86564371-86564381 chr2:86565005-86565019 chr2:86564247-86564256 chr2:86565017-86565030 chr2:86564904-86564917
13	POLR2A	chr2:86564571-86565111	ECC-1	luminal epithelium:	n/a	n/a
14	TAF1	chr2:86564542-86565087	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr2:86564912-86565217	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:86565038-86565088	NH-A	brain:	n/a
2	chr2:86565038-86565088	HAEpiC	amniotic membrane:	n/a
3	chr2:86565038-86565088	NHBE	bronchial:	n/a
4	chr2:86565038-86565088	HCM	heart:	n/a
5	chr2:86565038-86565088	K562	blood:	n/a
6	chr2:86565038-86565088	GM06990	blood:	n/a
7	chr2:86565038-86565088	MCF-7	breast:	n/a
8	chr2:86565038-86565088	HepG2	liver:	n/a
9	chr2:86565038-86565088	U87	brain:	n/a
10	chr2:86565038-86565088	NB4	blood:	n/a
11	chr2:86565038-86565088	T-47D	breast:	n/a
12	chr2:86565038-86565088	Hepatocyte	liver:	n/a
13	chr2:86565038-86565088	MCF10A-Er-Src	breast:	n/a
14	chr2:86565038-86565088	SAEC	small airway:	n/a
15	chr2:86565038-86565088	RPTEC	kidney:	n/a
16	chr2:86565038-86565088	HMEC	breast:	n/a
17	chr2:86565038-86565088	AG04449	skin:	fetal
18	chr2:86565038-86565088	BJ	skin:	n/a
19	chr2:86565038-86565088	GM19239	blood:	n/a
20	chr2:86565038-86565088	HRCEpiC	kidney:	n/a
21	chr2:86565038-86565088	GM12892	blood:	n/a
22	chr2:86565038-86565088	BE2_C	brain:	n/a
23	chr2:86565038-86565088	HCF	heart:	n/a
24	chr2:86565038-86565088	HUVEC	blood vessel:	n/a
25	chr2:86565038-86565088	HL-60	blood:	n/a
26	chr2:86565038-86565088	SK-N-SH_RA	brain:	n/a
27	chr2:86565038-86565088	CMK	blood:	n/a
28	chr2:86565038-86565088	HCT-116	colon:	n/a
29	chr2:86565038-86565088	PrEC	prostate:	n/a
30	chr2:86565038-86565088	PANC-1	pancreas:	n/a
31	chr2:86565038-86565088	Hela-S3	cervix:	n/a
32	chr2:86565038-86565088	ovcar-3	ovarian:	n/a
33	chr2:86565038-86565088	SKMC	muscle:	n/a
34	chr2:86565038-86565088	H1-hESC	embryonic stem cell:	embryo
35	chr2:86565038-86565088	LNCaP	prostate:	n/a
36	chr2:86565038-86565088	AG10803	skin:	n/a
37	chr2:86565038-86565088	GM12878	blood:	n/a
38	chr2:86565038-86565088	PFSK-1	brain:	n/a
39	chr2:86565038-86565088	ECC-1	luminal epithelium:	n/a
40	chr2:86565038-86565088	SK-N-SH	brain:	n/a
41	chr2:86565038-86565088	AG09319	gingival:	n/a
42	chr2:86565038-86565088	A549	lung:	n/a
43	chr2:86565038-86565088	IMR90	lung:	fetal
44	chr2:86565038-86565088	HRPEpiC	eye:	n/a
45	chr2:86565038-86565088	HCPEpiC	choroid plexus:	n/a
46	chr2:86565038-86565088	AG09309	skin:	n/a
47	chr2:86565038-86565088	NT2-D1	testis:	n/a
48	chr2:86565038-86565088	AG04450	lung:	fetal
49	chr2:86565038-86565088	NHDF-neo	bronchial:	n/a
50	chr2:86565038-86565088	HRE	kidney:	n/a

Variant related genes	Relation type
REEP1	TF binding region
REEP1	CpG island

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	esv3357801	chr2:86563266-86566214	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3448068	chr2:86563641-86565889	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86563000-86565200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr2:86563000-86565600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:86563400-86565600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:86563400-86565600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:86563600-86565200	Active TSS	Right Atrium	heart
6	chr2:86563600-86565200	Bivalent/Poised TSS	HSMM	muscle
7	chr2:86563600-86565400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr2:86563600-86565600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:86563600-86565600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:86563600-86565600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:86563800-86565200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:86563800-86565200	Active TSS	Aorta	Aorta
13	chr2:86563800-86565400	Bivalent/Poised TSS	Thymus	Thymus
14	chr2:86564000-86565200	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:86564000-86565200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
16	chr2:86564000-86565200	Active TSS	Gastric	stomach
17	chr2:86564000-86565200	Active TSS	Rectal Smooth Muscle	rectum
18	chr2:86564000-86565400	Active TSS	Right Ventricle	heart
19	chr2:86564000-86565600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr2:86564000-86565600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr2:86564200-86565200	Active TSS	Colon Smooth Muscle	Colon
22	chr2:86564200-86565200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr2:86564200-86565200	Bivalent/Poised TSS	NH-A	brain
24	chr2:86564200-86565400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:86564200-86565400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:86564200-86565600	Active TSS	Lung	lung
27	chr2:86564400-86565200	Enhancers	Liver	Liver
28	chr2:86564400-86565400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:86564800-86565200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:86564800-86565200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:86564800-86565200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:86564800-86565200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:86564800-86565200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
34	chr2:86564800-86565200	Flanking Bivalent TSS/Enh	HMEC	breast
35	chr2:86564800-86565400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
36	chr2:86564800-86565400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:86564800-86565400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86564800-86565400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:86564800-86565400	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr2:86564800-86565600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
46	chr2:86565000-86565200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
48	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr2:86565000-86565200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

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