Variant report

Variant	rs373188
Chromosome Location	chr3:120511490-120511491
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	chr3:120506049..120507948-chr3:120510885..120512477,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10511404	0.88[ASN][1000 genomes]
rs11714961	0.89[ASN][1000 genomes]
rs13316584	0.87[ASN][1000 genomes]
rs1566988	0.83[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs167722	0.91[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs172819	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178725	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292719	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs417061	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424044	0.83[ASN][1000 genomes]
rs4501055	0.83[ASN][1000 genomes]
rs519336	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55831173	0.87[ASN][1000 genomes]
rs56406902	0.87[ASN][1000 genomes]
rs607953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618642	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6778859	0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6796222	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs73183726	0.87[ASN][1000 genomes]
rs7620570	0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7633399	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9814744	0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs9838458	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs9854081	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs9872831	0.87[ASN][1000 genomes]
rs9985346	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]

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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1012541	chr3:120482402-120580319	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1014477	chr3:120482402-120583166	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr3:120482200-120517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:120483400-120521200	Weak transcription	Fetal Heart	heart
3	chr3:120499200-120515400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:120500600-120511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:120500600-120513000	Weak transcription	HepG2	liver
6	chr3:120501000-120513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:120501400-120513800	Weak transcription	A549	lung
8	chr3:120501400-120514400	Weak transcription	Fetal Intestine Large	intestine
9	chr3:120501600-120513800	Weak transcription	Liver	Liver
10	chr3:120502200-120512000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:120509200-120514400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:120509800-120514000	Enhancers	HUVEC	blood vessel
13	chr3:120510600-120511600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:120510600-120512000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:120510600-120512600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:120510600-120512800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:120510600-120512800	Enhancers	NHDF-Ad	bronchial
18	chr3:120510800-120512000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:120510800-120512800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:120510800-120513000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:120510800-120513200	Enhancers	NH-A	brain
22	chr3:120510800-120514400	Enhancers	Osteobl	bone
23	chr3:120511000-120511600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:120511000-120511600	Enhancers	NHEK	skin
25	chr3:120511000-120511800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:120511000-120512000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:120511000-120512200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:120511000-120512600	Enhancers	NHLF	lung
29	chr3:120511000-120513000	Enhancers	Hela-S3	cervix
30	chr3:120511200-120512400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:120511400-120512400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:120511400-120512400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:120511400-120513000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:120511400-120513600	Weak transcription	K562	blood
35	chr3:120511400-120514000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:120511400-120514000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:120511400-120516400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:120511400-120516800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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