Variant report

Variant	rs6796658
Chromosome Location	chr3:105218494-105218495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105215069..105217768-chr3:105217819..105220349,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10049426	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1036582	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10511243	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10933816	0.87[ASN][1000 genomes]
rs10933817	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12488994	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12491980	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12494392	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12695118	0.89[ASN][1000 genomes]
rs13062366	0.92[ASN][1000 genomes]
rs13064396	0.94[ASN][1000 genomes]
rs13092811	0.87[ASN][1000 genomes]
rs13097669	0.94[ASN][1000 genomes]
rs13100098	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1438538	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1438541	0.88[ASN][1000 genomes]
rs1530069	0.94[ASN][1000 genomes]
rs1898654	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2164956	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2178407	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2196745	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2399045	0.84[ASN][1000 genomes]
rs28670976	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2895299	0.94[ASN][1000 genomes]
rs4426702	0.87[ASN][1000 genomes]
rs4894831	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs57834585	0.94[ASN][1000 genomes]
rs6437587	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6437589	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6767277	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6767814	0.94[ASN][1000 genomes]
rs6769302	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6779807	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6780238	0.94[ASN][1000 genomes]
rs6806304	0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431531	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615005	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7629589	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7644273	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7647011	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7649033	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9288802	0.94[ASN][1000 genomes]
rs934856	0.94[ASN][1000 genomes]
rs975574	0.87[ASN][1000 genomes]
rs9842028	0.94[ASN][1000 genomes]
rs9851952	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9883620	0.80[ASN][1000 genomes]
rs9883799	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210000-105223000	Weak transcription	Gastric	stomach
2	chr3:105210200-105218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:105210200-105220600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:105210200-105220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:105210200-105221200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:105210200-105222000	Weak transcription	NH-A	brain
7	chr3:105210200-105223800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:105210200-105229000	Weak transcription	HSMM	muscle
9	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:105210400-105219600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:105210600-105219600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:105210600-105223200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:105210800-105222400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:105213800-105219600	Weak transcription	Aorta	Aorta
15	chr3:105214200-105218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:105214200-105220000	Weak transcription	Osteobl	bone
17	chr3:105214400-105218600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:105214400-105219600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:105214400-105220600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:105215000-105218600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:105215600-105218600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:105215600-105219600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:105215600-105219800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:105215600-105221200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:105215600-105223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:105215800-105218600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:105215800-105218600	Weak transcription	Fetal Lung	lung
28	chr3:105215800-105219200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:105215800-105223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:105215800-105223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:105217400-105220200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:105218200-105220600	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr3:105218200-105221200	Enhancers	HepG2	liver
34	chr3:105218200-105221400	Enhancers	Liver	Liver
35	chr3:105218200-105222000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:105218400-105218800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:105218400-105219200	Enhancers	Stomach Mucosa	stomach
38	chr3:105218400-105219800	Enhancers	A549	lung
39	chr3:105218400-105220200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:105218400-105220200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:105218400-105220200	Enhancers	Fetal Heart	heart

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