Variant report

Variant	rs28657821
Chromosome Location	chr16:80580813-80580814
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80580482..80583300-chr16:80838216..80840829,3	MCF-7	breast:
2	chr16:80573239..80577400-chr16:80578381..80583465,6	MCF-7	breast:
3	chr16:80573244..80577637-chr16:80578826..80581942,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166446	Chromatin interaction
ENSG00000259867	Chromatin interaction
ENSG00000168589	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10871389	0.89[EUR][1000 genomes]
rs10871390	0.89[EUR][1000 genomes]
rs11150295	0.87[EUR][1000 genomes]
rs11644889	1.00[ASN][1000 genomes]
rs11649558	1.00[ASN][1000 genomes]
rs11863816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866994	0.91[EUR][1000 genomes]
rs12051207	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102506	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443848	0.89[EUR][1000 genomes]
rs12444563	0.89[EUR][1000 genomes]
rs12445674	0.91[EUR][1000 genomes]
rs12597089	0.91[EUR][1000 genomes]
rs12597602	0.91[EUR][1000 genomes]
rs12598311	0.89[EUR][1000 genomes]
rs12600027	0.83[EUR][1000 genomes]
rs12934612	0.91[EUR][1000 genomes]
rs28448585	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531767	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542735	0.91[EUR][1000 genomes]
rs28581872	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583998	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28589320	0.91[EUR][1000 genomes]
rs28658033	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28668848	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683132	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302045	1.00[ASN][1000 genomes]
rs4334316	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352063	0.82[EUR][1000 genomes]
rs4458005	0.89[EUR][1000 genomes]
rs4517810	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4533296	0.89[EUR][1000 genomes]
rs4541087	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4567728	0.89[EUR][1000 genomes]
rs4622526	0.91[EUR][1000 genomes]
rs4889160	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs59416398	1.00[ASN][1000 genomes]
rs6564762	0.91[EUR][1000 genomes]
rs6564763	0.91[EUR][1000 genomes]
rs7187807	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7190759	0.91[EUR][1000 genomes]
rs73574279	0.87[ASN][1000 genomes]
rs8045496	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8182107	0.91[EUR][1000 genomes]
rs9929079	1.00[ASN][1000 genomes]
rs9931700	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932143	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933884	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940164	0.87[ASN][1000 genomes]
rs9972743	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972747	0.91[EUR][1000 genomes];1.00[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	nsv907001	chr16:80405292-80620611	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv833300	chr16:80475066-80601036	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80575400-80587200	Weak transcription	Pancreas	Pancrea
2	chr16:80575400-80587800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:80575800-80585800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr16:80578600-80585600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:80580800-80581800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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