Variant report

Variant	rs28558345
Chromosome Location	chr16:80581768-80581769
allele	A/G
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-3	chr16:80581739-80582081	ENSG00000260183.1

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10871389	0.87[ASN][1000 genomes]
rs10871390	0.87[ASN][1000 genomes]
rs11150295	0.87[ASN][1000 genomes]
rs11866994	0.87[ASN][1000 genomes]
rs12445674	0.91[ASN][1000 genomes]
rs12597089	0.91[ASN][1000 genomes]
rs12597602	0.91[ASN][1000 genomes]
rs12598311	0.88[ASN][1000 genomes]
rs12920691	0.88[ASN][1000 genomes]
rs12933306	0.88[ASN][1000 genomes]
rs12934612	0.91[ASN][1000 genomes]
rs28542735	0.89[ASN][1000 genomes]
rs28589320	0.89[ASN][1000 genomes]
rs4352063	0.85[ASN][1000 genomes]
rs4392091	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4392092	0.87[AMR][1000 genomes]
rs4458005	0.87[ASN][1000 genomes]
rs4530157	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533296	0.87[ASN][1000 genomes]
rs4567728	0.87[ASN][1000 genomes]
rs4577099	0.80[AMR][1000 genomes]
rs4622526	0.91[ASN][1000 genomes]
rs4889156	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889160	0.87[ASN][1000 genomes]
rs4996292	0.83[AMR][1000 genomes]
rs56879095	0.83[EUR][1000 genomes]
rs6564762	0.91[ASN][1000 genomes]
rs6564763	0.84[ASN][1000 genomes]
rs6564764	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7189457	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7190501	0.80[AMR][1000 genomes]
rs7190759	0.91[ASN][1000 genomes]
rs7192862	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7196394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7197982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044239	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8048886	0.80[AMR][1000 genomes]
rs8053848	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8059886	0.80[AMR][1000 genomes]
rs8182107	0.87[ASN][1000 genomes]
rs9806865	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806870	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806915	0.80[AMR][1000 genomes]
rs9806977	0.80[AMR][1000 genomes]
rs9928594	0.80[AMR][1000 genomes]
rs9935535	0.80[AMR][1000 genomes]
rs9937836	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938023	0.80[AMR][1000 genomes]
rs9939509	0.92[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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