Variant report

Variant	rs4683177
Chromosome Location	chr3:46126467-46126468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46126220..46128716-chr3:46205313..46206814,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1388605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388606	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388608	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1392288	0.90[CEU][hapmap]
rs1392293	0.85[EUR][1000 genomes]
rs1463680	0.83[CEU][hapmap]
rs1491949	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566419	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826342	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873616	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036293	0.83[EUR][1000 genomes]
rs2101446	0.82[EUR][1000 genomes]
rs2133666	0.86[EUR][1000 genomes]
rs2373148	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2373149	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373152	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373155	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4321566	0.82[EUR][1000 genomes]
rs4490404	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4493468	0.86[EUR][1000 genomes]
rs4682801	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4682811	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683158	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4683171	0.83[EUR][1000 genomes]
rs4683181	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786959	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6802312	1.00[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6807578	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808712	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809223	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7622333	0.95[CEU][hapmap]
rs7638309	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7653682	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs902760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904634	0.84[EUR][1000 genomes]
rs9311388	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875616	0.83[CEU][hapmap]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46120600-46127200	Weak transcription	Fetal Stomach	stomach
2	chr3:46120800-46127000	Weak transcription	HSMMtube	muscle
3	chr3:46120800-46129400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:46121400-46126800	Weak transcription	Fetal Thymus	thymus
5	chr3:46122600-46127000	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:46122800-46126600	Weak transcription	Ovary	ovary
7	chr3:46123000-46127600	Weak transcription	Hela-S3	cervix
8	chr3:46123200-46127000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:46123200-46129600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:46123400-46130400	Weak transcription	Adipose Nuclei	Adipose
11	chr3:46124600-46127000	Weak transcription	Fetal Lung	lung
12	chr3:46125000-46127200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:46125200-46127400	Weak transcription	Placenta	Placenta
14	chr3:46125400-46127800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:46125400-46128400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:46125800-46127000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:46125800-46127200	Weak transcription	HMEC	breast
18	chr3:46125800-46127400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:46125800-46127400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:46125800-46127800	Weak transcription	Fetal Heart	heart
21	chr3:46125800-46130600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:46126000-46127200	Weak transcription	NHEK	skin
23	chr3:46126200-46126600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:46126200-46126600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:46126200-46132600	Weak transcription	Right Atrium	heart

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