Variant report

Variant	rs11649558
Chromosome Location	chr16:80596945-80596946
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80589493..80592966-chr16:80593921..80596964,3	MCF-7	breast:
2	chr16:80595839..80600096-chr16:80600224..80603898,5	MCF-7	breast:
3	chr16:80576616..80579351-chr16:80593938..80597383,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-6	chr16:80596926-80597032	ENSG00000259867.1

Variant related genes	Relation type
ENSG00000168589	Chromatin interaction
ENSG00000260737	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10871390	0.81[CEU][hapmap]
rs11644215	1.00[CHB][hapmap]
rs11644889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11863816	1.00[ASN][1000 genomes]
rs11866588	1.00[ASN][1000 genomes]
rs11866734	0.85[CEU][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs12051207	1.00[ASN][1000 genomes]
rs12102506	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12443848	0.85[CEU][hapmap]
rs12444563	0.81[CEU][hapmap]
rs12444723	1.00[CHB][hapmap]
rs12934612	0.84[CEU][hapmap]
rs28448585	1.00[ASN][1000 genomes]
rs28531767	1.00[ASN][1000 genomes]
rs28581872	1.00[ASN][1000 genomes]
rs28583998	1.00[ASN][1000 genomes]
rs28657821	1.00[ASN][1000 genomes]
rs28668848	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28683132	1.00[ASN][1000 genomes]
rs28759267	1.00[ASN][1000 genomes]
rs4280255	0.81[CEU][hapmap]
rs4302045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4316772	0.88[EUR][1000 genomes]
rs4334316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59416398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187807	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs73574279	0.87[ASN][1000 genomes]
rs8045496	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs8182107	0.81[CEU][hapmap]
rs966669	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs966671	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9929079	1.00[ASN][1000 genomes]
rs9930879	0.83[AMR][1000 genomes]
rs9931700	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9932143	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9933884	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs9937215	0.82[AMR][1000 genomes]
rs9937217	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9940164	0.87[ASN][1000 genomes]
rs9972743	0.87[ASN][1000 genomes]
rs9972747	0.87[CEU][hapmap];1.00[CHB][hapmap];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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11649558	TERF2IP	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80596600-80597800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr16:80596800-80597600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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