Variant report

Variant	rs62263023
Chromosome Location	chr3:48260304-48260305
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48257660..48261585-chr3:48263263..48266797,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164047	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3731544	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3731553	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62260762	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62260779	1.00[ASN][1000 genomes]
rs62260785	1.00[ASN][1000 genomes]
rs62260788	1.00[ASN][1000 genomes]
rs62260850	1.00[ASN][1000 genomes]
rs62260855	1.00[ASN][1000 genomes]
rs62263027	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62263031	1.00[AFR][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	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 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	chr3:48251800-48264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:48255800-48261600	Enhancers	Adipose Nuclei	Adipose
3	chr3:48256200-48261600	Enhancers	Ovary	ovary
4	chr3:48256400-48260600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:48257400-48263400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:48257600-48264800	Weak transcription	Hela-S3	cervix
7	chr3:48257800-48272400	Weak transcription	Stomach Mucosa	stomach
8	chr3:48258200-48262800	Weak transcription	Left Ventricle	heart
9	chr3:48258200-48263800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:48258200-48264000	Weak transcription	Esophagus	oesophagus
11	chr3:48258800-48261000	Enhancers	Primary B cells from cord blood	blood
12	chr3:48259400-48261000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:48259400-48263600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:48259400-48265000	Weak transcription	Pancreas	Pancrea
15	chr3:48259400-48267400	Weak transcription	Right Ventricle	heart
16	chr3:48259600-48261400	Weak transcription	Lung	lung
17	chr3:48259600-48262800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:48260000-48260400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:48260000-48263200	Weak transcription	Spleen	Spleen
20	chr3:48260000-48274400	Weak transcription	Right Atrium	heart
21	chr3:48260200-48260400	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links