Variant report

Variant	rs4961680
Chromosome Location	chr9:16234930-16234931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16233531..16235152-chr9:16236701..16238739,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12002237	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12003973	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12003991	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16934286	0.83[ASN][1000 genomes]
rs16934287	0.83[ASN][1000 genomes]
rs4961468	0.81[ASN][1000 genomes]
rs4961469	0.83[ASN][1000 genomes]
rs4961471	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4961674	0.92[EUR][1000 genomes]
rs4961675	0.92[EUR][1000 genomes]
rs4961676	0.94[EUR][1000 genomes]
rs4961678	0.81[ASN][1000 genomes]
rs4961679	0.83[ASN][1000 genomes]
rs4961681	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4961683	0.92[ASN][1000 genomes]
rs56119294	0.83[ASN][1000 genomes]
rs57847950	0.83[ASN][1000 genomes]
rs59560725	0.93[ASN][1000 genomes]
rs73425617	0.92[EUR][1000 genomes]
rs73425648	0.93[ASN][1000 genomes]
rs9407728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9407729	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9407730	0.83[ASN][1000 genomes]
rs9407732	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9802651	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9802678	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv429999	chr9:16102066-16389100	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv892639	chr9:16190403-16242088	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv892640	chr9:16206695-16260837	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv892641	chr9:16218659-16242088	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv892642	chr9:16233085-16282979	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 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	chr9:16232800-16236000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:16233600-16235200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:16233600-16235400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:16233600-16235400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16234800-16235000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16234800-16235000	Enhancers	Right Ventricle	heart

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