Variant report

Variant	rs12662465
Chromosome Location	chr6:54586446-54586447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54583583..54586469-chr6:54727325..54729845,2	MCF-7	breast:
2	chr6:54585487..54587893-chr6:54738565..54741108,3	MCF-7	breast:
3	chr6:54584974..54587110-chr6:54788503..54790985,2	MCF-7	breast:
4	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
5	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
6	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
7	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
8	chr6:54585158..54588149-chr6:54741239..54743201,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1039495	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1039496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948840	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948844	0.90[ASN][1000 genomes]
rs10948846	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11967781	0.85[CHB][hapmap]
rs12525001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12525539	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12527042	0.92[ASN][1000 genomes]
rs12527077	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12527080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12527124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528881	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529275	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12661998	0.96[ASN][1000 genomes]
rs1395624	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1572593	0.81[EUR][1000 genomes]
rs1648201	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16869519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16885649	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16885656	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16885668	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16885735	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16885866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16885911	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16885948	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1948954	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1951693	0.80[EUR][1000 genomes]
rs1976539	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983140	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2048112	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048113	0.86[ASN][1000 genomes]
rs2894821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34752465	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35953958	0.94[ASN][1000 genomes]
rs4712068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712070	0.87[CHB][hapmap]
rs4715468	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715470	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715478	0.95[ASN][1000 genomes]
rs4994100	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58302712	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60501416	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs608873	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6459019	0.81[EUR][1000 genomes]
rs67799698	0.99[ASN][1000 genomes]
rs67875074	0.99[ASN][1000 genomes]
rs6915244	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73442093	0.86[ASN][1000 genomes]
rs73444113	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73444116	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73444125	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73446026	0.96[ASN][1000 genomes]
rs73446030	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73446036	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73446043	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7751908	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7761021	0.90[EUR][1000 genomes]
rs9349726	0.90[EUR][1000 genomes]
rs9370323	0.80[EUR][1000 genomes]
rs9474957	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54583600-54594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:54583800-54586600	Weak transcription	NHEK	skin
3	chr6:54584000-54586600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:54584600-54586600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:54585200-54587200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:54586400-54587200	Enhancers	HMEC	breast

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