Variant report

Variant	rs9289696
Chromosome Location	chr3:98676521-98676522
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98675333..98676915-chr3:98681651..98683756,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap]
rs12330381	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094707	1.00[ASN][1000 genomes]
rs13317610	0.86[EUR][1000 genomes]
rs13318536	1.00[ASN][1000 genomes]
rs13318960	0.93[ASN][1000 genomes]
rs13320266	0.86[EUR][1000 genomes]
rs13320890	1.00[CEU][hapmap]
rs13322253	1.00[CEU][hapmap]
rs13327449	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13327485	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1818053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2133575	0.87[ASN][1000 genomes]
rs2439232	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2439234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2454687	0.87[ASN][1000 genomes]
rs2470858	0.80[ASN][1000 genomes]
rs2470884	0.87[ASN][1000 genomes]
rs28528154	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28637457	1.00[ASN][1000 genomes]
rs28650813	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28821579	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28883308	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34693680	1.00[ASN][1000 genomes]
rs3796133	1.00[CEU][hapmap]
rs56172805	0.86[EUR][1000 genomes]
rs6795351	0.87[ASN][1000 genomes]
rs72938540	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs866873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9289699	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289700	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810407	0.86[EUR][1000 genomes]
rs9812438	1.00[CEU][hapmap]
rs9818215	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9819279	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819309	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828045	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9836915	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9838166	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9838238	1.00[CEU][hapmap]
rs9838706	1.00[CEU][hapmap]
rs9839559	1.00[CEU][hapmap]
rs9842226	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848335	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848583	1.00[CEU][hapmap]
rs9850469	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859042	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862660	1.00[CEU][hapmap]
rs9864010	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870500	1.00[CEU][hapmap]
rs9870940	0.88[EUR][1000 genomes]
rs9872073	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9872301	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9879302	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9883751	0.86[EUR][1000 genomes]
rs996199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv3440755	chr3:98666311-98680865	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98674000-98676800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:98674200-98677000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:98674200-98678800	Weak transcription	NH-A	brain
4	chr3:98674200-98679400	Weak transcription	NHLF	lung
5	chr3:98674200-98679600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:98674400-98677200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:98674400-98677600	Weak transcription	HMEC	breast
8	chr3:98674400-98679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:98674400-98679600	Weak transcription	Osteobl	bone
10	chr3:98674400-98681000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:98674600-98678800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:98675000-98679400	Weak transcription	NHDF-Ad	bronchial
13	chr3:98675200-98677600	Weak transcription	NHEK	skin
14	chr3:98675200-98680800	Weak transcription	Fetal Lung	lung
15	chr3:98675600-98677200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:98676000-98678000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:98676000-98678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:98676400-98679800	Enhancers	A549	lung

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