Variant report

Variant	rs3774344
Chromosome Location	chr3:51981021-51981022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51980605..51983550-chr3:51988202..51990542,2	MCF-7	breast:
2	chr3:51978894..51981977-chr3:52001614..52003382,3	MCF-7	breast:
3	chr3:51977575..51979816-chr3:51980206..51981763,2	K562	blood:
4	chr3:51976344..51977998-chr3:51978167..51981813,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180929	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];0.89[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876052	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188953	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2271069	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323864	0.86[ASN][1000 genomes]
rs323868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][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];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323893	1.00[CHB][hapmap];0.83[CHD][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];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs323898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56715917	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59682660	0.86[ASN][1000 genomes]
rs61546679	0.86[ASN][1000 genomes]
rs7611413	1.00[MEX][hapmap]
rs887541	0.82[YRI][hapmap]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51982000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:51977200-51983000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:51977200-51987600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:51977200-51989200	Weak transcription	Ovary	ovary
5	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
6	chr3:51977400-51981600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:51977400-51986200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:51977400-51987200	Weak transcription	Fetal Lung	lung
9	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
10	chr3:51977600-51981600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:51977600-51981600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:51977600-51982200	Weak transcription	NHLF	lung
13	chr3:51977600-51982400	Weak transcription	A549	lung
14	chr3:51977600-51982800	Weak transcription	GM12878-XiMat	blood
15	chr3:51977600-51983400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:51977600-51984400	Weak transcription	HepG2	liver
17	chr3:51977600-51986000	Weak transcription	Fetal Intestine Large	intestine
18	chr3:51977600-51987200	Weak transcription	HSMMtube	muscle
19	chr3:51977600-51987600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:51977600-51987600	Weak transcription	HSMM	muscle
21	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
23	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
24	chr3:51977800-51981600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:51977800-51983600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:51977800-51984000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:51977800-51985600	Weak transcription	Stomach Mucosa	stomach
28	chr3:51977800-51986000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:51977800-51987200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:51977800-51987800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:51978000-51982200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:51978200-51982400	Strong transcription	Fetal Intestine Small	intestine
34	chr3:51978200-51983400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:51978200-51983600	Strong transcription	Fetal Stomach	stomach
36	chr3:51978200-51983600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:51978200-51983600	Strong transcription	Spleen	Spleen
38	chr3:51978200-51983800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:51978200-51984200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:51978400-51982400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:51978400-51983400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:51978400-51984400	Strong transcription	Liver	Liver
43	chr3:51978600-51982800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:51978600-51983400	Strong transcription	Brain Anterior Caudate	brain
45	chr3:51978600-51983600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:51978800-51982400	Weak transcription	Placenta	Placenta
47	chr3:51978800-51983600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:51978800-51985200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:51978800-51987000	Weak transcription	Hela-S3	cervix
50	chr3:51979000-51982200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links