Variant report

Variant	rs10880573
Chromosome Location	chr12:44226111-44226112
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:44219284..44222535-chr12:44223504..44226954,3	MCF-7	breast:
2	chr12:44224786..44227179-chr12:44228814..44231665,3	MCF-7	breast:
3	chr12:44225134..44226705-chr12:44228557..44230915,2	K562	blood:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10506231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1057486	0.86[ASN][1000 genomes]
rs10736017	0.87[ASN][1000 genomes]
rs10748378	0.87[ASN][1000 genomes]
rs10785462	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10785463	0.87[ASN][1000 genomes]
rs10785466	0.87[ASN][1000 genomes]
rs10785471	0.85[GIH][hapmap]
rs10785472	0.85[GIH][hapmap]
rs10785474	0.85[GIH][hapmap]
rs10880578	0.84[ASN][1000 genomes]
rs10880585	0.87[ASN][1000 genomes]
rs10880586	0.85[GIH][hapmap]
rs10880598	0.85[GIH][hapmap]
rs10880605	0.85[GIH][hapmap]
rs11182273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11182293	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs11182324	0.87[ASN][1000 genomes]
rs11182325	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11182339	0.85[GIH][hapmap]
rs1358705	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1406787	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1609548	0.87[ASN][1000 genomes]
rs1609549	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1610291	0.87[ASN][1000 genomes]
rs1614042	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1621279	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1622590	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675755	0.82[GIH][hapmap]
rs1675756	0.87[ASN][1000 genomes]
rs1675758	0.87[ASN][1000 genomes]
rs1675764	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675765	0.87[ASN][1000 genomes]
rs1675767	0.87[ASN][1000 genomes]
rs1675769	0.87[ASN][1000 genomes]
rs1675772	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs1675781	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1675785	0.90[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1675787	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675789	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1675790	0.87[ASN][1000 genomes]
rs1731423	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731427	0.90[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1731429	0.86[ASN][1000 genomes]
rs1731430	0.87[ASN][1000 genomes]
rs1731431	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1731432	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs1731434	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731452	0.87[ASN][1000 genomes]
rs1731454	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731456	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731457	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731458	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1731459	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2219629	0.87[ASN][1000 genomes]
rs2407783	0.87[ASN][1000 genomes]
rs2447113	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2614394	0.90[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2951435	0.84[ASN][1000 genomes]
rs3764004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4238089	0.87[ASN][1000 genomes]
rs4238090	0.87[ASN][1000 genomes]
rs4238091	0.87[ASN][1000 genomes]
rs4354753	0.90[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4363674	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4469953	0.87[ASN][1000 genomes]
rs4537822	0.87[ASN][1000 genomes]
rs4572198	0.87[ASN][1000 genomes]
rs4572199	0.87[ASN][1000 genomes]
rs4609659	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4768052	0.81[ASN][1000 genomes]
rs4768053	0.90[CHB][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs4768538	0.87[ASN][1000 genomes]
rs4768543	0.81[ASN][1000 genomes]
rs5019975	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6582484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295151	0.87[ASN][1000 genomes]
rs7305609	0.87[ASN][1000 genomes]
rs73096934	0.87[ASN][1000 genomes]
rs7955615	0.90[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7964465	0.81[GIH][hapmap]
rs7971487	0.85[GIH][hapmap]
rs7972025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44223400-44227600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:44223400-44229000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:44223400-44229000	Weak transcription	Osteobl	bone
4	chr12:44223600-44228600	Weak transcription	Hela-S3	cervix
5	chr12:44223800-44228400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:44223800-44228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:44223800-44228800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:44223800-44229000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:44223800-44229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:44224000-44228600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:44224000-44229000	Weak transcription	NHEK	skin
12	chr12:44224200-44226400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:44224200-44228600	Weak transcription	Placenta	Placenta
14	chr12:44224200-44228800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:44224200-44229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:44224200-44229200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:44224800-44226400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:44224800-44227200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:44224800-44227200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:44225000-44227000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr12:44225000-44227200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:44225000-44227600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:44225000-44227800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:44225000-44229200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:44225200-44227600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:44225400-44227600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr12:44225600-44227000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:44225600-44227200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:44225800-44226200	Enhancers	Small Intestine	intestine
30	chr12:44225800-44227000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:44225800-44227000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr12:44225800-44227000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:44225800-44227200	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:44226000-44226200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:44226000-44226800	Enhancers	Thymus	Thymus
36	chr12:44226000-44227000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr12:44226000-44227000	Enhancers	Primary T cells from cord blood	blood
38	chr12:44226000-44227000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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