Variant report

Variant	rs2963340
Chromosome Location	chr5:8907028-8907029
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	chr2:200947698..200949239-chr5:8905135..8907032,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10044975	0.89[ASN][1000 genomes]
rs10066058	0.93[ASN][1000 genomes]
rs10067632	0.97[ASN][1000 genomes]
rs10067695	0.97[ASN][1000 genomes]
rs11743231	0.83[ASN][1000 genomes]
rs11747031	0.83[ASN][1000 genomes]
rs11955530	0.97[ASN][1000 genomes]
rs11960860	0.92[ASN][1000 genomes]
rs12519046	0.90[ASN][1000 genomes]
rs12522763	0.95[ASN][1000 genomes]
rs2962657	0.89[ASN][1000 genomes]
rs2962658	0.89[ASN][1000 genomes]
rs2962661	0.89[ASN][1000 genomes]
rs2962662	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962663	0.90[ASN][1000 genomes]
rs2962664	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962665	0.90[ASN][1000 genomes]
rs2962666	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962667	0.90[ASN][1000 genomes]
rs2962669	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962670	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2962674	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2962676	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2962677	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962679	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962681	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2963330	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963331	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963342	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963343	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963348	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963352	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963353	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963354	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963357	0.90[ASN][1000 genomes]
rs35444626	0.90[ASN][1000 genomes]
rs4298224	0.83[ASN][1000 genomes]
rs4701829	0.89[ASN][1000 genomes]
rs4701830	0.95[ASN][1000 genomes]
rs4701831	0.85[ASN][1000 genomes]
rs4702597	0.97[ASN][1000 genomes]
rs4702598	0.95[ASN][1000 genomes]
rs4702599	0.90[ASN][1000 genomes]
rs4702600	0.95[ASN][1000 genomes]
rs58276868	0.90[ASN][1000 genomes]
rs62356637	0.94[ASN][1000 genomes]
rs62356640	0.83[ASN][1000 genomes]
rs6872260	0.93[ASN][1000 genomes]
rs6875135	0.95[ASN][1000 genomes]
rs6875415	0.83[ASN][1000 genomes]
rs6889793	0.95[ASN][1000 genomes]
rs9313256	0.95[ASN][1000 genomes]
rs9313258	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	esv3492014	chr5:8749469-9004066	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3492015	chr5:8749469-9004066	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830199	chr5:8855056-9024096	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv482764	chr5:8906261-9056262	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:8904600-8908200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:8904600-8908600	Enhancers	NHLF	lung
3	chr5:8904600-8908800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:8904600-8908800	Enhancers	HMEC	breast
5	chr5:8904600-8908800	Enhancers	NHDF-Ad	bronchial
6	chr5:8904800-8907200	Enhancers	NHEK	skin
7	chr5:8904800-8907600	Enhancers	Osteobl	bone
8	chr5:8905200-8907600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:8905600-8907600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:8906000-8908800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:8906200-8908200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:8906400-8908200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:8906600-8908000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:8906600-8908000	Enhancers	HSMM	muscle
15	chr5:8906600-8908800	Enhancers	NH-A	brain
16	chr5:8906800-8907800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:8906800-8907800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:8907000-8907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:8907000-8907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:8907000-8908000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:8907000-8909000	Enhancers	Dnd41	blood

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