Variant report

Variant	rs12380227
Chromosome Location	chr9:17794026-17794027
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	chr9:17531556..17532244-chr9:17793906..17794864,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10448159	0.95[CEU][hapmap]
rs10491540	0.86[CEU][hapmap]
rs10738491	0.86[ASN][1000 genomes]
rs10810850	0.86[CEU][hapmap]
rs10963258	0.86[CEU][hapmap]
rs10963267	0.88[CEU][hapmap]
rs10963268	0.87[CEU][hapmap]
rs10963270	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963272	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10963273	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963274	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963275	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963276	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963278	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10963284	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10963288	0.81[EUR][1000 genomes]
rs10963289	0.82[EUR][1000 genomes]
rs10963295	0.90[ASN][1000 genomes]
rs10963299	0.90[ASN][1000 genomes]
rs1114790	0.95[CEU][hapmap]
rs12000241	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12006023	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12006056	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12377526	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12378332	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13290434	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13291009	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536068	0.95[CEU][hapmap]
rs16923365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16935984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2383041	0.83[CEU][hapmap]
rs2891113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34701669	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35728688	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35911294	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3808674	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4284123	1.00[ASN][1000 genomes]
rs4287033	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4382571	1.00[ASN][1000 genomes]
rs4394493	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4415416	0.90[ASN][1000 genomes]
rs4416918	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4430174	1.00[ASN][1000 genomes]
rs4477127	1.00[ASN][1000 genomes]
rs4481712	1.00[ASN][1000 genomes]
rs4487880	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4531142	1.00[ASN][1000 genomes]
rs4629969	1.00[ASN][1000 genomes]
rs4642745	0.90[ASN][1000 genomes]
rs4961448	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61551917	0.95[ASN][1000 genomes]
rs6475175	0.86[ASN][1000 genomes]
rs6475179	0.90[ASN][1000 genomes]
rs6475180	0.90[ASN][1000 genomes]
rs7024967	0.86[ASN][1000 genomes]
rs7027918	0.90[ASN][1000 genomes]
rs73642315	0.90[ASN][1000 genomes]
rs73645334	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73645339	1.00[ASN][1000 genomes]
rs7847592	0.90[ASN][1000 genomes]
rs7865921	0.81[CEU][hapmap]
rs7867642	0.90[ASN][1000 genomes]
rs7871893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7873468	0.90[ASN][1000 genomes]
rs9406734	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9406736	0.95[CEU][hapmap];0.82[EUR][1000 genomes]

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	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1034673	chr9:17739006-17916606	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1023089	chr9:17748811-17919574	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17784800-17799400	Weak transcription	Hela-S3	cervix
2	chr9:17787000-17800400	Weak transcription	Fetal Brain Female	brain
3	chr9:17788600-17805400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:17792800-17795400	Weak transcription	Brain Germinal Matrix	brain
5	chr9:17793400-17794200	Enhancers	Fetal Brain Male	brain
6	chr9:17794000-17795600	Weak transcription	Aorta	Aorta

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