Variant report

Variant	rs9968056
Chromosome Location	chr3:158888904-158888905
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158874720..158877859-chr3:158886349..158888915,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11917829	0.94[CEU][hapmap]
rs11920486	0.88[CEU][hapmap]
rs12696092	0.82[CEU][hapmap]
rs13059800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059834	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061579	0.83[CEU][hapmap]
rs13061619	0.83[CEU][hapmap]
rs13065679	0.83[CEU][hapmap]
rs13071140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075120	0.82[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13075790	0.88[CEU][hapmap]
rs13077258	0.83[CEU][hapmap]
rs13078847	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13079265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13080892	0.88[CEU][hapmap]
rs13082426	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083244	0.83[CEU][hapmap]
rs13083408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083887	0.88[CEU][hapmap]
rs13085008	0.82[CEU][hapmap]
rs13085667	0.83[CEU][hapmap]
rs13085707	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13088886	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091349	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13095658	0.94[CEU][hapmap]
rs13098336	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101053	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1448996	0.83[CEU][hapmap]
rs1449002	0.88[CEU][hapmap]
rs17795417	0.82[CEU][hapmap]
rs1839219	0.83[CEU][hapmap]
rs34066429	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34285329	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4328854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781001	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6781285	0.88[CEU][hapmap]
rs6784143	0.83[CEU][hapmap]
rs7619140	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620377	0.83[CEU][hapmap]
rs7644770	0.83[CEU][hapmap]
rs870852	0.88[CEU][hapmap]
rs9848338	0.82[CEU][hapmap]
rs9848831	0.82[CEU][hapmap]
rs9877316	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv491927	chr3:158692653-158952780	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1010828	chr3:158802474-158894319	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158884600-158889800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:158886600-158889400	Enhancers	HUVEC	blood vessel
3	chr3:158887400-158889000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:158887400-158889200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:158887400-158889200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:158887400-158889200	Enhancers	NHDF-Ad	bronchial
7	chr3:158887400-158889400	Enhancers	HSMMtube	muscle
8	chr3:158887400-158889400	Enhancers	NHLF	lung
9	chr3:158887400-158889600	Enhancers	Osteobl	bone
10	chr3:158887400-158890000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:158888200-158889400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:158888400-158889400	Enhancers	A549	lung
13	chr3:158888600-158889600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:158888600-158893000	Weak transcription	Stomach Mucosa	stomach
15	chr3:158888800-158889000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links