Variant report

Variant	rs12906606
Chromosome Location	chr15:54554225-54554226
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:54553109..54555656-chr15:54556214..54557724,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137766	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10518760	0.84[EUR][1000 genomes]
rs11071064	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11638986	0.83[CHB][hapmap];0.87[YRI][hapmap]
rs11856476	0.84[EUR][1000 genomes]
rs12899415	0.83[EUR][1000 genomes]
rs12899426	0.83[EUR][1000 genomes]
rs12901994	0.84[CEU][hapmap]
rs12902112	0.81[EUR][1000 genomes]
rs12902524	0.85[CHB][hapmap]
rs12903779	0.84[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12907062	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908083	0.85[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12908409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911007	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12911506	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12917198	0.83[CHB][hapmap]
rs1807348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414287	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414289	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34057643	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4517736	0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6493667	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68018837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172577	0.85[CHB][hapmap]
rs8024165	0.84[CEU][hapmap]
rs8025731	0.84[EUR][1000 genomes]
rs8026128	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs8028549	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036716	0.84[CEU][hapmap]
rs8037101	0.91[CHB][hapmap]
rs8039848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3362314	chr15:54551360-54556658	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54519000-54554400	Weak transcription	Aorta	Aorta
2	chr15:54547000-54652600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links