Variant report

Variant	rs540550863
Chromosome Location	chr3:51740932-51740933
allele	A/G
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	TAF1	chr3:51740825-51740993	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr3:51740765-51740994	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
3	MYC	chr3:51740848-51740978	MCF-7	breast:	n/a	n/a
4	REST	chr3:51740740-51740990	PANC-1	pancreas:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
5	POLR2A	chr3:51740787-51741033	K562	blood:	n/a	n/a
6	SP1	chr3:51740796-51741162	K562	blood:	n/a	chr3:51741027-51741038 chr3:51740950-51740961 chr3:51741010-51741021 chr3:51740998-51741009
7	REST	chr3:51740438-51741739	H1-neurons	neurons:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
8	RAD21	chr3:51740802-51740972	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:51740800-51740950	HA-sp	spinal cord:	n/a	n/a
10	HDAC2	chr3:51740779-51740985	HepG2	liver:	n/a	n/a
11	TAF1	chr3:51740824-51741410	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr3:51740811-51740982	K562	blood:	n/a	chr3:51740950-51740961
13	CTCF	chr3:51740840-51740990	HPF	lung:	n/a	n/a
14	REST	chr3:51740473-51741350	HL-60	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
15	REST	chr3:51740702-51741149	K562	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
16	REST	chr3:51740647-51740985	GM12878	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
17	CTCF	chr3:51740801-51740984	IMR90	lung:	n/a	n/a
18	E2F6	chr3:51740850-51741682	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:51740823-51741460	SK-N-MC	brain:	n/a	n/a
20	REST	chr3:51740410-51741624	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
21	MAZ	chr3:51740769-51741093	K562	blood:	n/a	chr3:51740769-51740778
22	MXI1	chr3:51740630-51741603	IMR90	lung:	n/a	n/a
23	SP4	chr3:51740778-51741000	H1-hESC	embryonic stem cell:	n/a	chr3:51740950-51740961 chr3:51740781-51740797
24	HDAC2	chr3:51740773-51740979	K562	blood:	n/a	n/a
25	REST	chr3:51740406-51741097	U87	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
26	TBP	chr3:51740818-51741572	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:51740820-51740970	AG04450	lung:	n/a	n/a
28	REST	chr3:51740652-51741144	HCT-116	colon:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
29	REST	chr3:51740522-51741200	MCF-7	breast:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
30	REST	chr3:51740757-51740993	Hela-S3	cervix:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
31	MAX	chr3:51740753-51741030	K562	blood:	n/a	chr3:51740769-51740778
32	POLR2A	chr3:51740868-51741318	MCF-7	breast:	n/a	n/a
33	SIN3AK20	chr3:51740756-51740986	SK-N-SH	brain:	n/a	n/a
34	CEBPD	chr3:51740798-51740998	HepG2	liver:	n/a	n/a
35	CTCF	chr3:51740849-51740970	Pancreas_OC	pancreas:	n/a	n/a
36	POLR2A	chr3:51740877-51741224	HUVEC	blood vessel:	n/a	n/a
37	JUND	chr3:51740800-51741027	H1-hESC	embryonic stem cell:	n/a	chr3:51740925-51740939
38	REST	chr3:51740528-51740999	Hela-S3	cervix:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
39	REST	chr3:51740757-51740990	GM12878	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51740897-51740906
40	POLR2A	chr3:51740805-51740979	K562	blood:	n/a	n/a
41	RCOR1	chr3:51740749-51741062	K562	blood:	n/a	n/a
42	MXI1	chr3:51740770-51741480	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3AK20	chr3:51740811-51740982	H1-hESC	embryonic stem cell:	n/a	n/a
44	RFX5	chr3:51740811-51740979	HepG2	liver:	n/a	n/a
45	CTCF	chr3:51740840-51740990	SAEC	small airway:	n/a	n/a
46	REST	chr3:51740538-51741286	HepG2	liver:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
47	MAX	chr3:51740729-51741152	MCF-7	breast:	n/a	chr3:51740769-51740778
48	FOXP2	chr3:51740810-51741008	PFSK-1	brain:	n/a	n/a
49	SP1	chr3:51740768-51741209	H1-hESC	embryonic stem cell:	n/a	chr3:51741027-51741038 chr3:51740950-51740961 chr3:51741010-51741021 chr3:51740783-51740792 chr3:51740781-51740793 chr3:51740782-51740796 chr3:51740998-51741009 chr3:51740781-51740793 chr3:51740782-51740792 chr3:51740782-51740791
50	YY1	chr3:51740848-51740981	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51740896-51740946	HepG2	liver:	n/a
2	chr3:51740896-51740946	GM12892	blood:	n/a
3	chr3:51740896-51740946	BE2_C	brain:	n/a
4	chr3:51740896-51740946	HEEpiC	esophagus:	n/a
5	chr3:51740896-51740946	RPTEC	kidney:	n/a
6	chr3:51740896-51740946	SK-N-SH_RA	brain:	n/a
7	chr3:51740896-51740946	AG09309	skin:	n/a
8	chr3:51740896-51740946	HMEC	breast:	n/a
9	chr3:51740896-51740946	CMK	blood:	n/a
10	chr3:51740896-51740946	ProgFib	skin:	n/a
11	chr3:51740896-51740946	LNCaP	prostate:	n/a
12	chr3:51740896-51740946	HNPCEpiC	eye:	n/a
13	chr3:51740896-51740946	GM06990	blood:	n/a
14	chr3:51740896-51740946	HUVEC	blood vessel:	n/a
15	chr3:51740896-51740946	HCM	heart:	n/a
16	chr3:51740896-51740946	HL-60	blood:	n/a
17	chr3:51740896-51740946	GM19239	blood:	n/a
18	chr3:51740896-51740946	HIPEpiC	eye:	n/a
19	chr3:51740896-51740946	SK-N-MC	brain:	n/a
20	chr3:51740896-51740946	NT2-D1	testis:	n/a
21	chr3:51740896-51740946	A549	lung:	n/a
22	chr3:51740896-51740946	AG09319	gingival:	n/a
23	chr3:51740896-51740946	AG04449	skin:	fetal
24	chr3:51740896-51740946	SK-N-SH	brain:	n/a
25	chr3:51740896-51740946	GM12891	blood:	n/a
26	chr3:51740896-51740946	Hela-S3	cervix:	n/a
27	chr3:51740896-51740946	BJ	skin:	n/a
28	chr3:51740896-51740946	H1-hESC	embryonic stem cell:	embryo
29	chr3:51740896-51740946	HCPEpiC	choroid plexus:	n/a
30	chr3:51740896-51740946	NB4	blood:	n/a
31	chr3:51740896-51740946	ECC-1	luminal epithelium:	n/a
32	chr3:51740896-51740946	Jurkat	blood:	n/a
33	chr3:51740896-51740946	PANC-1	pancreas:	n/a
34	chr3:51740896-51740946	PrEC	prostate:	n/a
35	chr3:51740896-51740946	HAEpiC	amniotic membrane:	n/a
36	chr3:51740896-51740946	IMR90	lung:	fetal
37	chr3:51740896-51740946	HRE	kidney:	n/a
38	chr3:51740896-51740946	AG10803	skin:	n/a
39	chr3:51740896-51740946	HRCEpiC	kidney:	n/a
40	chr3:51740896-51740946	U87	brain:	n/a
41	chr3:51740896-51740946	GM12878	blood:	n/a
42	chr3:51740896-51740946	Hepatocyte	liver:	n/a
43	chr3:51740896-51740946	AoSMC	blood vessel:	n/a
44	chr3:51740896-51740946	HPAEpiC	pulmonary alveolar:	n/a
45	chr3:51740896-51740946	MCF10A-Er-Src	breast:	n/a
46	chr3:51740896-51740946	Caco-2	colon:	n/a
47	chr3:51740896-51740946	T-47D	breast:	n/a
48	chr3:51740896-51740946	NH-A	brain:	n/a
49	chr3:51740896-51740946	HCT-116	colon:	n/a
50	chr3:51740896-51740946	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51739711..51741988-chr3:51976226..51978640,2	K562	blood:

Variant related genes	Relation type
GRM2	TF binding region
GRM2	CpG island
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3410055	chr3:51737012-51741510	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3403870	chr3:51740262-51741860	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51706400-51741000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:51716400-51741200	Weak transcription	Fetal Kidney	kidney
3	chr3:51719600-51741200	Weak transcription	NHDF-Ad	bronchial
4	chr3:51721000-51741000	Weak transcription	HUVEC	blood vessel
5	chr3:51722600-51741200	Weak transcription	Stomach Mucosa	stomach
6	chr3:51724400-51741200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:51733000-51741400	Weak transcription	Fetal Heart	heart
8	chr3:51734000-51741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:51734000-51741200	Weak transcription	NH-A	brain
10	chr3:51734600-51741400	Weak transcription	Fetal Lung	lung
11	chr3:51734600-51741600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:51735000-51741200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:51735200-51741200	Weak transcription	HepG2	liver
14	chr3:51735200-51741200	Weak transcription	Osteobl	bone
15	chr3:51736400-51741400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:51737000-51741200	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:51737400-51741200	Weak transcription	HMEC	breast
18	chr3:51738200-51741200	Weak transcription	Fetal Thymus	thymus
19	chr3:51738400-51741200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:51738400-51743400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:51738800-51741000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:51738800-51741000	Weak transcription	NHEK	skin
23	chr3:51738800-51741200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:51738800-51741200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:51738800-51741200	Weak transcription	Fetal Intestine Large	intestine
26	chr3:51738800-51741400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:51739000-51741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:51739000-51741000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:51739200-51741000	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:51739200-51741200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:51739400-51741000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:51739400-51741000	Weak transcription	Ovary	ovary
33	chr3:51739400-51741200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:51739400-51741200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:51739400-51741200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:51739400-51741200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:51739400-51741200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:51739400-51741200	Weak transcription	Left Ventricle	heart
39	chr3:51739400-51741200	Weak transcription	Thymus	Thymus
40	chr3:51739400-51741400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:51739400-51743400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:51739600-51741000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:51739600-51741000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:51739600-51741000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:51739600-51741200	Weak transcription	Brain Substantia Nigra	brain
46	chr3:51739600-51743600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:51739800-51741200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:51739800-51741200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:51739800-51741400	Weak transcription	Primary B cells from cord blood	blood
50	chr3:51739800-51741400	Weak transcription	Liver	Liver

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