Variant report

Variant	rs28562279
Chromosome Location	chr3:24638526-24638527
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	chr3:24631935..24633898-chr3:24636048..24638829,2	MCF-7	breast:
2	chr3:24536026..24537557-chr3:24637362..24639714,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10212332	0.92[ASN][1000 genomes]
rs10490837	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708042	0.81[EUR][1000 genomes]
rs11715809	0.90[EUR][1000 genomes]
rs13318800	0.82[EUR][1000 genomes]
rs1561079	0.82[ASN][1000 genomes]
rs17014900	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17014902	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1992040	0.82[EUR][1000 genomes]
rs2043579	0.88[EUR][1000 genomes]
rs2196434	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2196435	0.88[EUR][1000 genomes]
rs2196438	0.82[EUR][1000 genomes]
rs56135387	0.88[EUR][1000 genomes]
rs56268655	0.88[EUR][1000 genomes]
rs56281969	0.90[EUR][1000 genomes]
rs58152527	0.92[ASN][1000 genomes]
rs61701305	0.92[ASN][1000 genomes]
rs6550878	0.89[ASN][1000 genomes]
rs6550879	0.92[ASN][1000 genomes]
rs6767534	0.81[ASN][1000 genomes]
rs6767717	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6769209	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6770518	0.87[ASN][1000 genomes]
rs6771818	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6781066	0.89[ASN][1000 genomes]
rs6795607	0.88[ASN][1000 genomes]
rs6801494	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73038411	0.88[EUR][1000 genomes]
rs73038427	0.88[EUR][1000 genomes]
rs73040431	0.83[EUR][1000 genomes]
rs73040438	0.86[EUR][1000 genomes]
rs73040440	0.88[EUR][1000 genomes]
rs73040465	0.90[EUR][1000 genomes]
rs73040478	0.90[EUR][1000 genomes]
rs73040479	0.90[EUR][1000 genomes]
rs7647700	0.82[EUR][1000 genomes]
rs930317	0.93[ASN][1000 genomes]
rs9310745	0.81[EUR][1000 genomes]
rs9819865	0.93[ASN][1000 genomes]
rs9823545	0.82[EUR][1000 genomes]
rs9830859	0.88[ASN][1000 genomes]
rs9835497	0.81[EUR][1000 genomes]
rs9838616	0.82[EUR][1000 genomes]
rs9838720	0.82[EUR][1000 genomes]
rs9843609	0.82[EUR][1000 genomes]
rs9844544	0.82[EUR][1000 genomes]
rs9850781	0.82[EUR][1000 genomes]
rs9853927	0.82[EUR][1000 genomes]
rs9859978	0.90[ASN][1000 genomes]
rs9861129	0.82[EUR][1000 genomes]
rs9868375	0.88[ASN][1000 genomes]
rs9873830	0.81[EUR][1000 genomes]
rs9878606	0.93[ASN][1000 genomes]

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	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24630800-24640800	Weak transcription	Small Intestine	intestine
2	chr3:24632000-24640000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:24633200-24640000	Weak transcription	Fetal Lung	lung
4	chr3:24633600-24640000	Weak transcription	NHDF-Ad	bronchial
5	chr3:24633800-24639600	Weak transcription	HUVEC	blood vessel
6	chr3:24633800-24640200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:24634200-24640000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:24635600-24641400	Enhancers	HMEC	breast
9	chr3:24636000-24640000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:24636000-24640200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:24636800-24638800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:24637000-24641000	Enhancers	NHEK	skin
13	chr3:24637200-24638600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:24637200-24639000	Enhancers	Fetal Intestine Large	intestine
15	chr3:24637400-24639800	Weak transcription	Stomach Mucosa	stomach
16	chr3:24637800-24640000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:24638000-24639600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:24638400-24638600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:24638400-24639200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:24638400-24639400	Weak transcription	Hela-S3	cervix

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