Variant report

Variant	rs4960006
Chromosome Location	chr6:4593822-4593823
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	chr6:4587247..4590668-chr6:4591336..4594466,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11751457	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756102	0.91[CEU][hapmap]
rs11962754	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964426	0.91[CEU][hapmap]
rs17138527	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17138534	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17138543	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143455	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235724	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235726	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235727	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs377207	1.00[ASN][1000 genomes]
rs378901	1.00[ASN][1000 genomes]
rs385236	1.00[ASN][1000 genomes]
rs385884	1.00[ASN][1000 genomes]
rs390126	1.00[ASN][1000 genomes]
rs390617	1.00[ASN][1000 genomes]
rs400405	1.00[ASN][1000 genomes]
rs413716	1.00[ASN][1000 genomes]
rs418563	1.00[ASN][1000 genomes]
rs421930	1.00[ASN][1000 genomes]
rs424137	1.00[ASN][1000 genomes]
rs438021	1.00[ASN][1000 genomes]
rs453768	1.00[ASN][1000 genomes]
rs4959306	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4960004	1.00[ASN][1000 genomes]
rs4960005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601192	1.00[ASN][1000 genomes]
rs62384944	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6911463	0.91[CEU][hapmap];1.00[GIH][hapmap]
rs6913171	1.00[ASN][1000 genomes]
rs7764724	0.84[EUR][1000 genomes]
rs84996	0.82[EUR][1000 genomes]
rs9328261	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9328262	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9502199	1.00[ASN][1000 genomes]
rs9502200	1.00[ASN][1000 genomes]
rs9502202	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502204	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502205	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502206	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502208	1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs9504151	1.00[ASN][1000 genomes]
rs9504152	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504154	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504156	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504159	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504160	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504163	0.81[EUR][1000 genomes]
rs9504165	0.91[CEU][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv883415	chr6:4546491-4629654	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4582400-4595400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:4590000-4594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:4590000-4594000	Weak transcription	HMEC	breast
4	chr6:4590000-4594000	Weak transcription	NHEK	skin
5	chr6:4590200-4594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:4593800-4594000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:4593800-4594400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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