Variant report

Variant	rs143304581
Chromosome Location	chr3:52269737-52269738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52269409-52269872	GM12878	blood:	n/a	n/a
2	MAX	chr3:52269608-52269961	NB4	blood:	n/a	chr3:52269846-52269856 chr3:52269823-52269833
3	POLR2A	chr3:52269660-52269955	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52269736-52269786	NT2-D1	testis:	n/a
2	chr3:52269736-52269786	GM12878	blood:	n/a
3	chr3:52269736-52269786	GM12891	blood:	n/a
4	chr3:52269736-52269786	HCM	heart:	n/a
5	chr3:52269736-52269786	SKMC	muscle:	n/a
6	chr3:52269736-52269786	HL-60	blood:	n/a
7	chr3:52269736-52269786	ECC-1	luminal epithelium:	n/a
8	chr3:52269736-52269786	ovcar-3	ovarian:	n/a
9	chr3:52269736-52269786	SK-N-SH_RA	brain:	n/a
10	chr3:52269736-52269786	HUVEC	blood vessel:	n/a
11	chr3:52269736-52269786	A549	lung:	n/a
12	chr3:52269736-52269786	AoSMC	blood vessel:	n/a
13	chr3:52269736-52269786	Hela-S3	cervix:	n/a
14	chr3:52269736-52269786	PANC-1	pancreas:	n/a
15	chr3:52269736-52269786	GM19239	blood:	n/a
16	chr3:52269736-52269786	NHDF-neo	bronchial:	n/a
17	chr3:52269736-52269786	U87	brain:	n/a
18	chr3:52269736-52269786	HEEpiC	esophagus:	n/a
19	chr3:52269736-52269786	T-47D	breast:	n/a
20	chr3:52269736-52269786	CMK	blood:	n/a
21	chr3:52269736-52269786	GM06990	blood:	n/a
22	chr3:52269736-52269786	HMEC	breast:	n/a
23	chr3:52269736-52269786	AG04449	skin:	fetal
24	chr3:52269736-52269786	GM12892	blood:	n/a
25	chr3:52269736-52269786	PFSK-1	brain:	n/a
26	chr3:52269736-52269786	NB4	blood:	n/a
27	chr3:52269736-52269786	NH-A	brain:	n/a
28	chr3:52269736-52269786	HCF	heart:	n/a
29	chr3:52269736-52269786	HAEpiC	amniotic membrane:	n/a
30	chr3:52269736-52269786	LNCaP	prostate:	n/a
31	chr3:52269736-52269786	BJ	skin:	n/a
32	chr3:52269736-52269786	HEK293	kidney:	embryo
33	chr3:52269736-52269786	ProgFib	skin:	n/a
34	chr3:52269736-52269786	SK-N-MC	brain:	n/a
35	chr3:52269736-52269786	HCPEpiC	choroid plexus:	n/a
36	chr3:52269736-52269786	AG10803	skin:	n/a
37	chr3:52269736-52269786	HNPCEpiC	eye:	n/a
38	chr3:52269736-52269786	HRPEpiC	eye:	n/a
39	chr3:52269736-52269786	RPTEC	kidney:	n/a
40	chr3:52269736-52269786	BE2_C	brain:	n/a
41	chr3:52269736-52269786	HRCEpiC	kidney:	n/a
42	chr3:52269736-52269786	HRE	kidney:	n/a
43	chr3:52269736-52269786	Hepatocyte	liver:	n/a
44	chr3:52269736-52269786	Jurkat	blood:	n/a
45	chr3:52269736-52269786	IMR90	lung:	fetal
46	chr3:52269736-52269786	K562	blood:	n/a
47	chr3:52269736-52269786	SAEC	small airway:	n/a
48	chr3:52269736-52269786	AG09319	gingival:	n/a
49	chr3:52269736-52269786	H1-hESC	embryonic stem cell:	embryo
50	chr3:52269736-52269786	HIPEpiC	eye:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52269274..52272214-chr3:52398381..52400803,2	K562	blood:
2	chr3:52259472..52263342-chr3:52269626..52274061,4	MCF-7	breast:
3	chr3:52262902..52264608-chr3:52269630..52271396,2	K562	blood:
4	chr3:52268502..52270036-chr3:52311908..52314756,2	K562	blood:
5	chr3:52265696..52268496-chr3:52269267..52272971,4	MCF-7	breast:
6	chr3:52268721..52271141-chr3:52272963..52274697,2	K562	blood:
7	chr3:52268278..52270898-chr3:52320244..52322252,2	K562	blood:
8	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
9	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
10	chr3:52269288..52271694-chr3:52319110..52321005,2	MCF-7	breast:
11	chr3:52269533..52276077-chr3:52310385..52313504,11	MCF-7	breast:
12	chr3:52257505..52260127-chr3:52268132..52270399,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000243224	TF binding region
TWF2	TF binding region
ENSG00000173366	TF binding region
ENSG00000173366	CpG island
ENSG00000243224	CpG island
TWF2	CpG island
ENSG00000239732	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000173366	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
4	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:52261600-52270600	Strong transcription	NHEK	skin
8	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:52261800-52270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:52262400-52269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:52262400-52269800	Strong transcription	Osteobl	bone
14	chr3:52262400-52270000	Strong transcription	NHLF	lung
15	chr3:52263000-52269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:52264200-52271400	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr3:52264600-52270000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:52264800-52270600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52265000-52270400	Weak transcription	K562	blood
20	chr3:52265000-52272000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:52265200-52270400	Weak transcription	HSMMtube	muscle
22	chr3:52265200-52270800	Weak transcription	HUVEC	blood vessel
23	chr3:52265400-52269800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:52265400-52270800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:52265400-52271800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:52265600-52270400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:52265600-52270400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52265600-52270400	Strong transcription	Fetal Intestine Small	intestine
29	chr3:52265600-52270400	Weak transcription	Stomach Mucosa	stomach
30	chr3:52265600-52270400	Weak transcription	HMEC	breast
31	chr3:52265600-52270600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:52265600-52270600	Weak transcription	Small Intestine	intestine
33	chr3:52265600-52270800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:52265600-52270800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:52265600-52271200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:52265800-52270000	Genic enhancers	Primary T cells from cord blood	blood
37	chr3:52265800-52270000	Genic enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:52265800-52271600	Enhancers	Liver	Liver
39	chr3:52266000-52270600	Weak transcription	NH-A	brain
40	chr3:52266000-52271400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:52266000-52271600	Weak transcription	Fetal Lung	lung
42	chr3:52266200-52269800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:52266200-52269800	Strong transcription	Esophagus	oesophagus
44	chr3:52266200-52270000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:52266200-52270600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:52266200-52271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:52266400-52271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:52266600-52270400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52266600-52270400	Weak transcription	HSMM	muscle
50	chr3:52266600-52272200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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