Variant report

Variant	rs4352063
Chromosome Location	chr16:80586720-80586721
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80573756..80576188-chr16:80586618..80589955,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259867	Chromatin interaction
ENSG00000168589	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10871389	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10871390	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11150295	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11863816	0.82[EUR][1000 genomes]
rs11866588	0.82[EUR][1000 genomes]
rs11866734	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs11866994	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12051207	0.90[EUR][1000 genomes]
rs12102506	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs12443848	0.86[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12444563	0.92[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12445674	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12597089	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12597602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12598311	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12600027	0.89[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12920691	0.94[ASN][1000 genomes]
rs12933306	0.94[ASN][1000 genomes]
rs12934612	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28448585	0.83[EUR][1000 genomes]
rs28531767	0.87[EUR][1000 genomes]
rs28542735	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28558345	0.85[ASN][1000 genomes]
rs28581872	0.89[EUR][1000 genomes]
rs28583998	0.84[EUR][1000 genomes]
rs28589320	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28657821	0.82[EUR][1000 genomes]
rs28658033	0.89[EUR][1000 genomes]
rs28668848	0.90[EUR][1000 genomes]
rs28683132	0.90[EUR][1000 genomes]
rs28759267	0.82[EUR][1000 genomes]
rs4392091	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4427819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4458005	0.93[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4517810	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4530157	0.85[ASN][1000 genomes]
rs4533296	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4534859	0.84[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap]
rs4567728	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4622526	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889160	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4889161	0.84[EUR][1000 genomes]
rs6564762	0.93[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564763	0.93[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564764	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7185063	0.83[ASN][1000 genomes]
rs7187807	0.81[EUR][1000 genomes]
rs7190759	0.93[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7192862	0.81[ASN][1000 genomes]
rs7196394	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7197982	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8182107	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806865	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9931700	0.82[EUR][1000 genomes]
rs9932143	0.82[EUR][1000 genomes]
rs9933884	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9935465	0.87[YRI][hapmap]
rs9937217	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9937836	0.85[ASN][1000 genomes]
rs9938023	0.86[CHB][hapmap]
rs9939509	0.85[ASN][1000 genomes]
rs9972743	0.90[EUR][1000 genomes]
rs9972747	0.82[CEU][hapmap];0.90[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4352063	TERF2IP	cis	parietal	SCAN
rs4352063	C16orf61	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr16:80585800-80586800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr16:80585800-80586800	Enhancers	HMEC	breast
5	chr16:80585800-80586800	Flanking Active TSS	NHEK	skin
6	chr16:80585800-80590800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr16:80586400-80586800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:80586400-80587000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:80586600-80587800	Weak transcription	Fetal Muscle Leg	muscle
10	chr16:80586600-80588000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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