Variant report

Variant	rs11563197
Chromosome Location	chr2:234960021-234960022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234492023-234494396..2:234954947-234965240	Hela-S3	cervix:
2	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000228949	Chromatin interaction
ENSG00000224287	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10929333	0.94[ASN][1000 genomes]
rs11562947	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11884288	1.00[ASN][1000 genomes]
rs11885740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1507517	1.00[ASN][1000 genomes]
rs1507518	1.00[ASN][1000 genomes]
rs1507519	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17864799	1.00[ASN][1000 genomes]
rs17864800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17864801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17865702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17865707	1.00[ASN][1000 genomes]
rs17865708	1.00[ASN][1000 genomes]
rs17866610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17869095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17869099	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28903699	1.00[ASN][1000 genomes]
rs28903985	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs28904000	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28904005	0.96[ASN][1000 genomes]
rs34179683	0.91[ASN][1000 genomes]
rs35211354	0.98[ASN][1000 genomes]
rs7585488	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1006053	chr2:234941290-234963441	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	nsv1007335	chr2:234941290-234964316	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
6	nsv1001846	chr2:234943285-234963541	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
7	nsv10224	chr2:234959698-234962384	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234959400-234961000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:234959400-234961000	Enhancers	NHDF-Ad	bronchial
3	chr2:234959400-234961400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:234959600-234960600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:234959600-234961200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:234959800-234960200	Active TSS	Liver	Liver
7	chr2:234959800-234960600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:234959800-234961400	Enhancers	NHEK	skin
9	chr2:234960000-234960400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:234960000-234960400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:234960000-234960600	Enhancers	HMEC	breast
12	chr2:234960000-234960600	Enhancers	NH-A	brain
13	chr2:234960000-234961400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links