Variant report

Variant	rs665535
Chromosome Location	chr2:234956934-234956935
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:234956720-234957112	MCF10A-Er-Src	breast:	n/a	n/a
2	BCL3	chr2:234956735-234956972	GM12878	blood:	n/a	n/a
3	FOS	chr2:234956771-234957120	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:234956777-234957056	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr2:234956813-234957036	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr2:234956783-234957086	MCF10A-Er-Src	breast:	n/a	n/a
7	BCL3	chr2:234956693-234957108	GM12878	blood:	n/a	n/a
8	STAT3	chr2:234956823-234957122	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr2:234956785-234957050	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	2:234492023-234494396..2:234954947-234965240	Hela-S3	cervix:
2	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:
3	chr2:234835606..234837772-chr2:234955390..234957030,2	K562	blood:

Variant related genes	Relation type
SPP2	TF binding region
ENSG00000228949	Chromatin interaction
ENSG00000224287	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10178472	0.89[AMR][1000 genomes]
rs10192448	0.88[AMR][1000 genomes]
rs10193392	0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs10195232	0.83[AMR][1000 genomes]
rs10197450	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10200368	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs10207367	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10210816	0.89[AMR][1000 genomes]
rs10803669	0.91[AMR][1000 genomes]
rs13389896	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13395783	0.88[AMR][1000 genomes]
rs17864802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17864805	0.91[AMR][1000 genomes]
rs17869100	0.91[AMR][1000 genomes]
rs1911595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2267901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3819748	0.89[AMR][1000 genomes]
rs4664004	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs596463	0.84[EUR][1000 genomes]
rs620654	0.84[EUR][1000 genomes]
rs622060	0.84[EUR][1000 genomes]
rs634613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7593927	0.99[ASN][1000 genomes]
rs9636245	0.89[AMR][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	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

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234956000-234957200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:234956000-234957200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:234956600-234957200	Enhancers	HMEC	breast
4	chr2:234956600-234959400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:234956800-234959400	Weak transcription	NHDF-Ad	bronchial
6	chr2:234956800-234959600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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