Variant report

Variant	rs544422490
Chromosome Location	chr3:51741139-51741140
allele	C/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	SP1	chr3:51740796-51741162	K562	blood:	n/a	chr3:51741027-51741038 chr3:51740950-51740961 chr3:51741010-51741021 chr3:51740998-51741009
2	REST	chr3:51740438-51741739	H1-neurons	neurons:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
3	TAF1	chr3:51740824-51741410	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr3:51740473-51741350	HL-60	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
5	REST	chr3:51740702-51741149	K562	blood:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
6	E2F6	chr3:51740850-51741682	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:51740823-51741460	SK-N-MC	brain:	n/a	n/a
8	REST	chr3:51740410-51741624	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
9	MXI1	chr3:51740630-51741603	IMR90	lung:	n/a	n/a
10	REST	chr3:51741051-51741222	K562	blood:	n/a	chr3:51741059-51741072
11	TBP	chr3:51740818-51741572	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr3:51740652-51741144	HCT-116	colon:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
13	REST	chr3:51740522-51741200	MCF-7	breast:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
14	POLR2A	chr3:51740868-51741318	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:51740877-51741224	HUVEC	blood vessel:	n/a	n/a
16	MXI1	chr3:51740770-51741480	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZBTB7A	chr3:51741003-51741439	ECC-1	luminal epithelium:	n/a	n/a
18	REST	chr3:51740538-51741286	HepG2	liver:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
19	MAX	chr3:51740729-51741152	MCF-7	breast:	n/a	chr3:51740769-51740778
20	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
21	CREB1	chr3:51740786-51741151	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr3:51740204-51741740	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
23	REST	chr3:51740663-51741142	HCT-116	colon:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
24	REST	chr3:51739816-51741537	SK-N-SH	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
25	REST	chr3:51740712-51741250	HepG2	liver:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
26	TAF7	chr3:51740777-51741292	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:51740745-51741379	H1-neurons	neurons:	n/a	n/a
28	MAX	chr3:51740682-51741445	ECC-1	luminal epithelium:	n/a	chr3:51740769-51740778
29	TEAD4	chr3:51740627-51741181	A549	lung:	n/a	n/a
30	POLR2A	chr3:51741056-51741260	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr3:51740643-51741480	ECC-1	luminal epithelium:	n/a	chr3:51740769-51740778
32	REST	chr3:51741034-51741252	GM12878	blood:	n/a	chr3:51741059-51741072
33	REST	chr3:51740775-51741185	SK-N-SH	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
34	POLR2A	chr3:51740885-51741462	MCF-7	breast:	n/a	n/a
35	MAX	chr3:51740794-51741623	H1-hESC	embryonic stem cell:	n/a	n/a
36	REST	chr3:51740283-51741145	ECC-1	luminal epithelium:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
37	ZNF263	chr3:51740825-51741351	HEK293-T-REx	kidney:	n/a	n/a
38	REST	chr3:51741083-51741284	SK-N-SH	brain:	n/a	n/a
39	TAF1	chr3:51741024-51741287	H1-hESC	embryonic stem cell:	n/a	n/a
40	REST	chr3:51740477-51741284	PANC-1	pancreas:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
41	REST	chr3:51740063-51741723	PFSK-1	brain:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
42	POLR2A	chr3:51741034-51741407	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:51740788-51741608	H1-neurons	neurons:	n/a	n/a
44	REST	chr3:51740699-51741211	H1-neurons	neurons:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740897-51740906
45	REST	chr3:51740070-51741651	H1-hESC	embryonic stem cell:	n/a	chr3:51740882-51740900 chr3:51740900-51740910 chr3:51740881-51740895 chr3:51741059-51741072 chr3:51740250-51740259 chr3:51740897-51740906
46	E2F6	chr3:51740935-51741594	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:51741021-51741305	ECC-1	luminal epithelium:	n/a	n/a
48	GABPA	chr3:51741042-51741448	H1-hESC	embryonic stem cell:	n/a	chr3:51741075-51741084
49	POLR2A	chr3:51741074-51741314	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAZ	chr3:51740612-51741318	IMR90	lung:	n/a	chr3:51740769-51740778

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51741135-51741185	AG09319	gingival:	n/a
2	chr3:51741135-51741185	GM19239	blood:	n/a
3	chr3:51741135-51741185	Hela-S3	cervix:	n/a
4	chr3:51741135-51741185	MCF-7	breast:	n/a
5	chr3:51741135-51741185	HCF	heart:	n/a
6	chr3:51741135-51741185	ovcar-3	ovarian:	n/a
7	chr3:51741135-51741185	HIPEpiC	eye:	n/a
8	chr3:51741135-51741185	NB4	blood:	n/a
9	chr3:51741135-51741185	BE2_C	brain:	n/a
10	chr3:51741135-51741185	GM12878	blood:	n/a
11	chr3:51741135-51741185	ECC-1	luminal epithelium:	n/a
12	chr3:51741135-51741185	HepG2	liver:	n/a
13	chr3:51741135-51741185	HEK293	kidney:	embryo
14	chr3:51741135-51741185	NHDF-neo	bronchial:	n/a
15	chr3:51741135-51741185	SK-N-MC	brain:	n/a
16	chr3:51741135-51741185	BJ	skin:	n/a
17	chr3:51741135-51741185	RPTEC	kidney:	n/a
18	chr3:51741135-51741185	HRE	kidney:	n/a
19	chr3:51741135-51741185	PrEC	prostate:	n/a
20	chr3:51741135-51741185	AG04450	lung:	fetal
21	chr3:51741135-51741185	GM12891	blood:	n/a
22	chr3:51741135-51741185	HCPEpiC	choroid plexus:	n/a
23	chr3:51741135-51741185	AoSMC	blood vessel:	n/a
24	chr3:51741135-51741185	HPAEpiC	pulmonary alveolar:	n/a
25	chr3:51741135-51741185	SAEC	small airway:	n/a
26	chr3:51741135-51741185	A549	lung:	n/a
27	chr3:51741135-51741185	HUVEC	blood vessel:	n/a
28	chr3:51741135-51741185	Jurkat	blood:	n/a
29	chr3:51741135-51741185	HEEpiC	esophagus:	n/a
30	chr3:51741135-51741185	CMK	blood:	n/a
31	chr3:51741135-51741185	HMEC	breast:	n/a
32	chr3:51741135-51741185	Caco-2	colon:	n/a
33	chr3:51741135-51741185	SK-N-SH_RA	brain:	n/a
34	chr3:51741135-51741185	SKMC	muscle:	n/a
35	chr3:51741135-51741185	HCM	heart:	n/a
36	chr3:51741135-51741185	LNCaP	prostate:	n/a
37	chr3:51741135-51741185	NT2-D1	testis:	n/a
38	chr3:51741135-51741185	HNPCEpiC	eye:	n/a
39	chr3:51741135-51741185	AG04449	skin:	fetal
40	chr3:51741135-51741185	H1-hESC	embryonic stem cell:	embryo
41	chr3:51741135-51741185	MCF10A-Er-Src	breast:	n/a
42	chr3:51741135-51741185	AG09309	skin:	n/a
43	chr3:51741135-51741185	AG10803	skin:	n/a
44	chr3:51741135-51741185	HAEpiC	amniotic membrane:	n/a
45	chr3:51741135-51741185	T-47D	breast:	n/a
46	chr3:51741135-51741185	IMR90	lung:	fetal
47	chr3:51741135-51741185	ProgFib	skin:	n/a
48	chr3:51741135-51741185	HRPEpiC	eye:	n/a
49	chr3:51741135-51741185	U87	brain:	n/a
50	chr3:51741135-51741185	GM12892	blood:	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51716400-51741200	Weak transcription	Fetal Kidney	kidney
2	chr3:51719600-51741200	Weak transcription	NHDF-Ad	bronchial
3	chr3:51722600-51741200	Weak transcription	Stomach Mucosa	stomach
4	chr3:51724400-51741200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:51733000-51741400	Weak transcription	Fetal Heart	heart
6	chr3:51734000-51741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:51734000-51741200	Weak transcription	NH-A	brain
8	chr3:51734600-51741400	Weak transcription	Fetal Lung	lung
9	chr3:51734600-51741600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:51735000-51741200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:51735200-51741200	Weak transcription	HepG2	liver
12	chr3:51735200-51741200	Weak transcription	Osteobl	bone
13	chr3:51736400-51741400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:51737000-51741200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:51737400-51741200	Weak transcription	HMEC	breast
16	chr3:51738200-51741200	Weak transcription	Fetal Thymus	thymus
17	chr3:51738400-51741200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:51738400-51743400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:51738800-51741200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:51738800-51741200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:51738800-51741200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:51738800-51741400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:51739200-51741200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:51739400-51741200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:51739400-51741200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:51739400-51741200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:51739400-51741200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:51739400-51741200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:51739400-51741200	Weak transcription	Left Ventricle	heart
30	chr3:51739400-51741200	Weak transcription	Thymus	Thymus
31	chr3:51739400-51741400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:51739400-51743400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:51739600-51741200	Weak transcription	Brain Substantia Nigra	brain
34	chr3:51739600-51743600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:51739800-51741200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:51739800-51741200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:51739800-51741400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:51739800-51741400	Weak transcription	Liver	Liver
39	chr3:51740000-51741200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:51740000-51741200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:51740000-51741200	Enhancers	Fetal Brain Male	brain
42	chr3:51740000-51741400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:51740000-51741600	Weak transcription	Aorta	Aorta
44	chr3:51740000-51744200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:51740200-51741200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:51740200-51741200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:51740200-51741200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:51740200-51741200	Weak transcription	Esophagus	oesophagus
49	chr3:51740200-51741200	Weak transcription	Gastric	stomach
50	chr3:51740200-51741200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links