Variant report

Variant	rs7856477
Chromosome Location	chr9:16602654-16602655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16154369..16155237-chr9:16601764..16602655,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10116857	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10117448	1.00[CEU][hapmap]
rs10120281	0.84[EUR][1000 genomes]
rs10121959	0.83[AMR][1000 genomes]
rs10123480	1.00[CEU][hapmap]
rs10123558	0.82[CEU][hapmap]
rs10511622	1.00[CEU][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10733312	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10738437	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs10738439	1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756763	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10810576	0.82[CEU][hapmap]
rs10962492	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs10962493	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10962494	0.82[CEU][hapmap];0.84[LWK][hapmap]
rs10962511	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12000426	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12002673	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs12337676	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12338548	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs12343239	0.83[AMR][1000 genomes]
rs12343306	0.83[AMR][1000 genomes]
rs12350242	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12350853	0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs12352543	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1337391	0.86[YRI][hapmap]
rs1337393	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1337400	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1415473	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1415474	1.00[CEU][hapmap]
rs1415475	0.86[EUR][1000 genomes]
rs1415476	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16934842	0.84[EUR][1000 genomes]
rs1927616	1.00[CEU][hapmap]
rs1927617	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs1927618	0.82[CEU][hapmap]
rs1927626	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1952345	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs1952346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2065937	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2149159	0.83[EUR][1000 genomes]
rs2382808	1.00[CEU][hapmap]
rs2382809	1.00[CEU][hapmap]
rs2382810	1.00[CEU][hapmap]
rs28490464	0.84[EUR][1000 genomes]
rs28733737	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2891072	1.00[CEU][hapmap]
rs3739716	1.00[CHB][hapmap]
rs4961725	0.83[EUR][1000 genomes]
rs6475059	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs6475060	1.00[CEU][hapmap]
rs6475062	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs6475063	0.83[AMR][1000 genomes]
rs7018877	0.83[EUR][1000 genomes]
rs7019016	0.83[EUR][1000 genomes]
rs7019105	0.83[EUR][1000 genomes]
rs7029578	1.00[CHD][hapmap]
rs7030387	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7032772	0.81[EUR][1000 genomes]
rs7048399	0.90[EUR][1000 genomes]
rs7049082	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs725011	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7350234	1.00[CEU][hapmap]
rs7470623	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7850123	0.82[CEU][hapmap]
rs7854979	0.83[EUR][1000 genomes]
rs7858025	0.82[CEU][hapmap]
rs7863885	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs7870380	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs7870508	0.81[EUR][1000 genomes]
rs7872747	0.91[AMR][1000 genomes]
rs7872838	0.91[AMR][1000 genomes]
rs943745	1.00[CEU][hapmap]

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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv524264	chr9:16596071-16611692	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16583000-16606800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16583200-16611200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:16586800-16604400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:16595000-16611200	Weak transcription	NHLF	lung
5	chr9:16597600-16604400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:16597600-16610800	Weak transcription	Fetal Stomach	stomach
7	chr9:16598800-16608200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:16598800-16611400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:16599000-16603600	Weak transcription	A549	lung
10	chr9:16599000-16607000	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:16599000-16612200	Weak transcription	Osteobl	bone
12	chr9:16599000-16612600	Weak transcription	HSMM	muscle
13	chr9:16601200-16602800	Enhancers	Ovary	ovary
14	chr9:16601200-16604200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:16601400-16602800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr9:16602200-16607800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:16602400-16602800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:16602400-16603400	Enhancers	Dnd41	blood
19	chr9:16602400-16608000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:16602600-16602800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:16602600-16603000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:16602600-16603200	Enhancers	HUVEC	blood vessel
23	chr9:16602600-16608800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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