Variant report

Variant	rs62254714
Chromosome Location	chr3:84597575-84597576
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	chr3:84597130..84597691-chr3:85409635..85410581,3	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]
rs12488651	1.00[ASN][1000 genomes]
rs1473461	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586307	0.86[ASN][1000 genomes]
rs17492563	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17500476	0.86[EUR][1000 genomes]
rs1905846	0.91[ASN][1000 genomes]
rs1905848	0.86[ASN][1000 genomes]
rs56985130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59551717	0.95[ASN][1000 genomes]
rs59671531	0.96[ASN][1000 genomes]
rs62254217	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62254685	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62254689	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62254715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781297	1.00[ASN][1000 genomes]
rs6782948	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73127115	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644089	0.86[ASN][1000 genomes]
rs7646863	0.86[ASN][1000 genomes]
rs9309944	0.96[ASN][1000 genomes]
rs974534	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs974535	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9825859	0.86[ASN][1000 genomes]
rs9837600	0.92[ASN][1000 genomes]
rs9839147	0.95[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	nsv1007008	chr3:84069044-84653896	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv536612	chr3:84069044-84653896	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460743	chr3:84094818-84644186	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv590814	chr3:84094818-84644186	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2760745	chr3:84208364-84783259	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv998578	chr3:84521514-84773582	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv536615	chr3:84521514-84773582	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv460744	chr3:84526413-84630305	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv590850	chr3:84526413-84630305	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84596200-84597800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:84597000-84598400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:84597200-84597600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:84597200-84597600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:84597200-84597600	Flanking Active TSS	Liver	Liver
6	chr3:84597200-84597600	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:84597200-84597600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:84597200-84597600	Enhancers	Left Ventricle	heart
9	chr3:84597200-84597600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:84597200-84597800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:84597200-84597800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:84597200-84597800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:84597200-84597800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:84597200-84597800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:84597200-84597800	Enhancers	Brain Substantia Nigra	brain
16	chr3:84597200-84597800	Flanking Active TSS	HepG2	liver
17	chr3:84597200-84598400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:84597200-84598400	Active TSS	A549	lung
19	chr3:84597400-84597800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:84597400-84597800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:84597400-84597800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:84597400-84597800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:84597400-84597800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr3:84597400-84597800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:84597400-84597800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:84597400-84597800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr3:84597400-84597800	Enhancers	Brain Hippocampus Middle	brain
28	chr3:84597400-84597800	Enhancers	Placenta	Placenta
29	chr3:84597400-84597800	Flanking Active TSS	Pancreas	Pancrea
30	chr3:84597400-84598000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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