Variant report

Variant	rs17864689
Chromosome Location	chr2:234594234-234594235
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234473821..234476593-chr2:234593192..234596119,2	MCF-7	breast:
2	chr2:234593709..234597691-chr2:234598690..234601824,5	MCF-7	breast:
3	chr2:234464967..234466988-chr2:234593051..234595705,2	MCF-7	breast:
4	chr2:234395319..234396920-chr2:234593778..234595799,2	MCF-7	breast:
5	chr2:234590200..234591773-chr2:234592005..234594297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000244122	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11568318	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1551286	0.84[EUR][1000 genomes]
rs17862835	0.84[EUR][1000 genomes]
rs17862844	0.84[EUR][1000 genomes]
rs17862846	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17862848	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17862851	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862854	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862859	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17862874	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863784	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17863795	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863800	0.81[EUR][1000 genomes]
rs17864666	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17864670	0.89[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs17864671	0.84[EUR][1000 genomes]
rs17864675	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17864691	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868298	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17868299	0.84[EUR][1000 genomes]
rs17868301	0.84[EUR][1000 genomes]
rs17868318	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17868320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868338	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17868341	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17874945	0.81[EUR][1000 genomes]
rs28898590	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34916116	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45507691	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56125405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56143032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714486	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6755571	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563478	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7585521	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	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
5	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234588600-234597000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:234590000-234597800	Weak transcription	Colonic Mucosa	Colon
3	chr2:234590800-234597400	Weak transcription	Liver	Liver
4	chr2:234590800-234599800	Weak transcription	Esophagus	oesophagus
5	chr2:234591600-234597000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:234592400-234597200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:234592600-234595600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:234592600-234597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:234593000-234594400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:234593200-234598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:234594200-234595000	Weak transcription	A549	lung

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