Variant report

Variant	rs3755797
Chromosome Location	chr3:51998125-51998126
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	SIN3AK20	chr3:51998118-51998444	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr3:51998014-51998456	H1-hESC	embryonic stem cell:	n/a	chr3:51998261-51998271
3	SIN3A	chr3:51998103-51998494	H1-hESC	embryonic stem cell:	n/a	chr3:51998455-51998466
4	POLR2A	chr3:51997165-51999885	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51970192..51973030-chr3:51997697..51999602,2	K562	blood:
2	chr3:51992685..51994681-chr3:51997289..51999303,2	MCF-7	breast:
3	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
4	chr3:51997651..51999473-chr3:52171714..52174151,2	K562	blood:

Variant related genes	Relation type
PCBP4	TF binding region
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11926611	0.89[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051957	0.82[CHB][hapmap]
rs1876052	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188953	0.85[EUR][1000 genomes]
rs2271069	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323864	0.86[ASN][1000 genomes]
rs323868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323874	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323881	0.89[ASN][1000 genomes]
rs323885	0.89[ASN][1000 genomes]
rs323886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323894	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3774344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4416372	0.82[CHB][hapmap]
rs4986825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56715917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59682660	0.86[ASN][1000 genomes]
rs61546679	0.86[ASN][1000 genomes]
rs9833784	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9860982	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3365586	chr3:51995312-51998710	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix
2	chr3:51990600-52000200	Weak transcription	NHDF-Ad	bronchial
3	chr3:51990600-52000400	Weak transcription	Small Intestine	intestine
4	chr3:51990600-52000400	Weak transcription	HUVEC	blood vessel
5	chr3:51990600-52000800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:51990800-51999600	Weak transcription	NH-A	brain
7	chr3:51990800-52000400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:51991000-51999600	Weak transcription	Colonic Mucosa	Colon
9	chr3:51991000-51999600	Weak transcription	HMEC	breast
10	chr3:51991000-51999800	Weak transcription	NHEK	skin
11	chr3:51991000-52000200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:51991000-52000400	Weak transcription	Stomach Mucosa	stomach
13	chr3:51991000-52000600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:51991200-52000000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:51991200-52000400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:51991200-52000400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:51991400-52000200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:51991800-51998200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:51992800-52000400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:51993400-52000400	Weak transcription	Osteobl	bone
21	chr3:51994000-52000200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:51994600-51998600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:51994600-51999800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:51994600-52000800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:51994800-51999200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:51994800-51999400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:51995000-51998200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:51995000-51999000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:51995000-51999600	Weak transcription	Adipose Nuclei	Adipose
30	chr3:51995000-52000200	Weak transcription	Esophagus	oesophagus
31	chr3:51995000-52000400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:51995200-51998200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:51995200-51999200	Weak transcription	Lung	lung
34	chr3:51995200-51999800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:51995400-51998400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:51995400-51998800	Weak transcription	Gastric	stomach
37	chr3:51995400-51999400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:51995400-52000600	Enhancers	Left Ventricle	heart
39	chr3:51995600-51998400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:51995600-51998800	Enhancers	Ovary	ovary
41	chr3:51995600-51999600	Enhancers	HepG2	liver
42	chr3:51995600-52000400	Enhancers	Right Atrium	heart
43	chr3:51995800-51999200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:51995800-51999400	Genic enhancers	Fetal Stomach	stomach
45	chr3:51995800-51999600	Enhancers	Psoas Muscle	Psoas
46	chr3:51995800-52000200	Enhancers	Fetal Muscle Leg	muscle
47	chr3:51996000-51998400	Enhancers	Brain Substantia Nigra	brain
48	chr3:51996000-51998800	Enhancers	Fetal Muscle Trunk	muscle
49	chr3:51996000-51999200	Weak transcription	Aorta	Aorta
50	chr3:51996200-52000200	Enhancers	Right Ventricle	heart

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