Variant report

Variant	rs9820089
Chromosome Location	chr3:81539406-81539407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:81538877..81541023-chr3:81682087..81685020,2	MCF-7	breast:
2	chr3:81538965..81540197-chr3:81692644..81693504,4	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11917955	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs11918127	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs11920137	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920270	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922101	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs13320194	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs13433893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1461607	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17019144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17019176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1984974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009766	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228389	0.91[ASN][1000 genomes]
rs2291593	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs28415702	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28478451	0.91[ASN][1000 genomes]
rs28702560	0.91[ASN][1000 genomes]
rs28780766	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs3821555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs55828412	0.89[ASN][1000 genomes]
rs58339236	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58977050	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59161789	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60844651	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6762839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6766394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6774605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72904318	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72904375	0.95[ASN][1000 genomes]
rs72904388	0.89[ASN][1000 genomes]
rs72904392	0.89[ASN][1000 genomes]
rs72904402	0.89[ASN][1000 genomes]
rs73853334	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7617859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs7619190	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs7629051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652717	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9309873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs9813324	0.95[ASN][1000 genomes]
rs9815184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9822535	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823178	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9823236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9823805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9825828	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828209	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9828883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848657	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9854820	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862555	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9865935	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868543	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878273	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs998205	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs998207	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934018	chr3:81413060-81655338	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv999587	chr3:81534364-81707800	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv536603	chr3:81534364-81707800	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81532600-81540000	Weak transcription	Left Ventricle	heart
2	chr3:81532600-81540000	Weak transcription	Right Ventricle	heart
3	chr3:81534000-81547200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:81535000-81539600	Weak transcription	Ovary	ovary
5	chr3:81535000-81539800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:81535000-81540000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:81535000-81540200	Weak transcription	Fetal Heart	heart
8	chr3:81535000-81541600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:81535200-81539600	Weak transcription	NHLF	lung
10	chr3:81535200-81541600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:81535200-81545600	Weak transcription	Psoas Muscle	Psoas
12	chr3:81535200-81549000	Weak transcription	Colonic Mucosa	Colon
13	chr3:81535200-81553000	Weak transcription	Aorta	Aorta
14	chr3:81535200-81555600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:81535200-81563200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:81535200-81566800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:81535400-81539600	Weak transcription	Fetal Lung	lung
18	chr3:81535400-81540000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:81535400-81540000	Weak transcription	Osteobl	bone
20	chr3:81535400-81540800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:81535400-81540800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:81535400-81565600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:81535400-81579400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:81535600-81539600	Weak transcription	NHDF-Ad	bronchial
25	chr3:81535600-81579400	Weak transcription	HUVEC	blood vessel
26	chr3:81536800-81540400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:81537200-81539800	Weak transcription	Right Atrium	heart
28	chr3:81537600-81540800	Weak transcription	Liver	Liver
29	chr3:81537600-81545400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:81537800-81539600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:81538000-81540200	Strong transcription	HSMM	muscle
32	chr3:81538200-81541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:81538800-81543400	Strong transcription	Dnd41	blood
34	chr3:81539000-81539800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:81539000-81545600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:81539400-81540000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:81539400-81540000	Weak transcription	Gastric	stomach
38	chr3:81539400-81540400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:81539400-81553000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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