Variant report

Variant	rs12961966
Chromosome Location	chr18:12552632-12552633
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12541118..12543753-chr18:12550923..12553850,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10445428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080583	0.98[ASN][1000 genomes]
rs11080584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080585	0.81[ASN][1000 genomes]
rs11080586	0.82[ASN][1000 genomes]
rs11659854	0.81[ASN][1000 genomes]
rs11663958	0.82[ASN][1000 genomes]
rs11664861	0.83[ASN][1000 genomes]
rs11664914	0.83[ASN][1000 genomes]
rs11664917	0.83[ASN][1000 genomes]
rs11664936	0.81[ASN][1000 genomes]
rs11665543	0.81[ASN][1000 genomes]
rs12326271	0.80[ASN][1000 genomes]
rs12454931	0.82[ASN][1000 genomes]
rs12455093	0.92[ASN][1000 genomes]
rs12455536	0.87[ASN][1000 genomes]
rs12455909	0.85[ASN][1000 genomes]
rs12457903	0.96[ASN][1000 genomes]
rs12604385	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12604400	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12604541	0.82[ASN][1000 genomes]
rs12605240	0.85[ASN][1000 genomes]
rs12605392	0.83[ASN][1000 genomes]
rs12606506	0.89[ASN][1000 genomes]
rs12709540	0.90[ASN][1000 genomes]
rs12953406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954614	0.90[ASN][1000 genomes]
rs12955161	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12955490	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12956385	0.86[ASN][1000 genomes]
rs12956885	0.84[ASN][1000 genomes]
rs12957151	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12957688	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12958200	0.82[ASN][1000 genomes]
rs12959015	0.89[ASN][1000 genomes]
rs12961695	0.87[ASN][1000 genomes]
rs12962476	0.85[ASN][1000 genomes]
rs12963179	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12963325	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12964660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12965094	0.89[ASN][1000 genomes]
rs12970025	0.82[ASN][1000 genomes]
rs12970174	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1893193	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1940974	0.85[ASN][1000 genomes]
rs1940975	0.81[ASN][1000 genomes]
rs2155698	0.81[ASN][1000 genomes]
rs2186907	0.82[ASN][1000 genomes]
rs28414067	0.82[ASN][1000 genomes]
rs28496036	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28582228	0.82[ASN][1000 genomes]
rs28886423	0.85[ASN][1000 genomes]
rs34072260	0.89[ASN][1000 genomes]
rs34178879	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34456643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34814556	0.91[ASN][1000 genomes]
rs34899007	0.89[ASN][1000 genomes]
rs35122110	0.88[ASN][1000 genomes]
rs35449211	0.87[ASN][1000 genomes]
rs35630805	0.83[ASN][1000 genomes]
rs35963756	0.97[ASN][1000 genomes]
rs4389196	0.85[ASN][1000 genomes]
rs4493131	0.88[ASN][1000 genomes]
rs4627434	0.81[ASN][1000 genomes]
rs55749182	0.98[ASN][1000 genomes]
rs58215411	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60505421	0.99[ASN][1000 genomes]
rs62097094	0.86[ASN][1000 genomes]
rs62097102	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62097103	0.94[ASN][1000 genomes]
rs62097126	0.85[ASN][1000 genomes]
rs62097148	0.83[ASN][1000 genomes]
rs62097149	0.81[ASN][1000 genomes]
rs62097153	0.82[ASN][1000 genomes]
rs67045810	0.82[ASN][1000 genomes]
rs67268432	0.97[ASN][1000 genomes]
rs722708	0.87[ASN][1000 genomes]
rs7234697	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723836	0.88[ASN][1000 genomes]
rs7238546	0.82[ASN][1000 genomes]
rs7242395	0.87[ASN][1000 genomes]
rs755020	0.83[ASN][1000 genomes]
rs755021	0.83[ASN][1000 genomes]
rs8086094	0.83[ASN][1000 genomes]
rs8087885	0.88[ASN][1000 genomes]
rs8088786	0.82[ASN][1000 genomes]
rs8089081	0.87[ASN][1000 genomes]
rs8089619	0.98[ASN][1000 genomes]
rs8093129	0.84[ASN][1000 genomes]
rs8093571	0.86[ASN][1000 genomes]
rs8095160	0.81[ASN][1000 genomes]
rs948301	0.83[ASN][1000 genomes]
rs948302	0.83[ASN][1000 genomes]
rs9675543	0.83[ASN][1000 genomes]
rs9945339	0.82[ASN][1000 genomes]
rs9947738	0.82[ASN][1000 genomes]
rs9951147	0.85[ASN][1000 genomes]
rs9959759	0.85[ASN][1000 genomes]
rs9961851	0.83[ASN][1000 genomes]
rs9964759	0.83[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12516000-12553200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:12516600-12555000	Weak transcription	Aorta	Aorta
3	chr18:12541400-12553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr18:12545200-12553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr18:12545600-12553000	Weak transcription	Psoas Muscle	Psoas
6	chr18:12546800-12557000	Weak transcription	Ovary	ovary
7	chr18:12551600-12553800	Enhancers	HMEC	breast
8	chr18:12551800-12553000	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr18:12551800-12553200	Enhancers	Brain Angular Gyrus	brain
10	chr18:12551800-12553400	Enhancers	Stomach Mucosa	stomach
11	chr18:12551800-12553600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr18:12551800-12553600	Enhancers	Adipose Nuclei	Adipose
13	chr18:12551800-12553600	Enhancers	Right Ventricle	heart
14	chr18:12551800-12553600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr18:12551800-12553600	Enhancers	HepG2	liver
16	chr18:12551800-12553800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:12551800-12553800	Enhancers	Left Ventricle	heart
18	chr18:12551800-12553800	Enhancers	Lung	lung
19	chr18:12552000-12553600	Enhancers	Esophagus	oesophagus
20	chr18:12552200-12553400	Enhancers	Brain Cingulate Gyrus	brain
21	chr18:12552200-12554200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr18:12552400-12552800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr18:12552400-12553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr18:12552400-12553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:12552400-12553000	Weak transcription	Right Atrium	heart
26	chr18:12552400-12553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:12552400-12553200	Enhancers	Brain Anterior Caudate	brain
28	chr18:12552400-12553200	Enhancers	Osteobl	bone
29	chr18:12552400-12553600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:12552400-12553600	Enhancers	Brain Hippocampus Middle	brain
31	chr18:12552400-12553800	Enhancers	Liver	Liver
32	chr18:12552400-12554800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr18:12552400-12555800	Weak transcription	HSMMtube	muscle
34	chr18:12552400-12556600	Weak transcription	NHDF-Ad	bronchial
35	chr18:12552400-12557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:12552400-12557200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr18:12552400-12557800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr18:12552400-12559600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:12552400-12560000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:12552600-12553000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr18:12552600-12553000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr18:12552600-12553200	Weak transcription	Fetal Brain Female	brain
43	chr18:12552600-12553400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr18:12552600-12553400	Weak transcription	Brain Substantia Nigra	brain
45	chr18:12552600-12556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:12552600-12557000	Weak transcription	Pancreas	Pancrea
47	chr18:12552600-12558000	Weak transcription	Stomach Smooth Muscle	stomach

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