Variant report

Variant	rs10871390
Chromosome Location	chr16:80573920-80573921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:80573873-80574995	GM12891	blood:	n/a	n/a
2	HCFC1	chr16:80573472-80575175	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:80573239..80577400-chr16:80578381..80583465,6	MCF-7	breast:
2	chr16:80573192..80575392-chr16:80605742..80608359,2	MCF-7	breast:
3	chr16:80573111..80574963-chr16:80576346..80580119,3	K562	blood:
4	chr16:80572758..80574587-chr16:80801032..80802655,2	MCF-7	breast:
5	chr16:80573487..80575142-chr16:80836688..80838672,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-6	chr16:80573869-80574385	XLOC_012019

No data

Variant related genes	Relation type
DYNLRB2	TF binding region
ENSG00000168589	Chromatin interaction
ENSG00000166446	Chromatin interaction
ENSG00000260737	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10871389	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150295	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649558	0.81[CEU][hapmap]
rs11863816	0.88[EUR][1000 genomes]
rs11866588	0.88[EUR][1000 genomes]
rs11866734	0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs11866994	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12051207	0.83[EUR][1000 genomes]
rs12102506	0.82[EUR][1000 genomes]
rs12443848	0.95[CEU][hapmap];0.88[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12444563	0.90[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12445674	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12597089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12597602	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12598311	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12600027	0.80[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12920691	0.99[ASN][1000 genomes]
rs12933306	0.99[ASN][1000 genomes]
rs12934612	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28448585	0.87[EUR][1000 genomes]
rs28531767	0.85[EUR][1000 genomes]
rs28542735	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28558345	0.87[ASN][1000 genomes]
rs28583998	0.86[EUR][1000 genomes]
rs28589320	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28657821	0.89[EUR][1000 genomes]
rs28668848	0.81[EUR][1000 genomes]
rs28683132	0.82[EUR][1000 genomes]
rs28759267	0.89[EUR][1000 genomes]
rs4280255	1.00[CEU][hapmap]
rs4352063	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]
rs4392091	0.93[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4427819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4458005	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517810	0.81[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4530157	0.87[ASN][1000 genomes]
rs4533296	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534859	0.87[YRI][hapmap]
rs4541087	0.88[EUR][1000 genomes]
rs4567728	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889160	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564762	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6564763	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564764	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7185063	0.88[ASN][1000 genomes]
rs7187807	0.85[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7190759	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7192862	0.88[ASN][1000 genomes]
rs7196394	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7197982	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8045496	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs8182107	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806865	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9931700	0.89[EUR][1000 genomes]
rs9932143	0.81[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs9933884	0.81[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs9935465	0.87[YRI][hapmap]
rs9937217	0.87[EUR][1000 genomes]
rs9937836	0.87[ASN][1000 genomes]
rs9938023	0.86[CHB][hapmap]
rs9939509	0.87[ASN][1000 genomes]
rs9972743	0.82[EUR][1000 genomes]
rs9972747	0.83[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
rs10871390	TERF2IP	cis	parietal	SCAN
rs10871390	C16orf61	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80573600-80574000	Active TSS	Brain Angular Gyrus	brain
2	chr16:80573600-80574400	Active TSS	Primary hematopoietic stem cells	blood
3	chr16:80573800-80574000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr16:80573800-80574000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr16:80573800-80574000	Enhancers	Liver	Liver
6	chr16:80573800-80574000	ZNF genes & repeats	GM12878-XiMat	blood
7	chr16:80573800-80574000	Enhancers	NHEK	skin
8	chr16:80573800-80574200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr16:80573800-80574200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr16:80573800-80574200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:80573800-80574200	Bivalent/Poised TSS	Fetal Brain Male	brain
12	chr16:80573800-80574200	Enhancers	Fetal Kidney	kidney
13	chr16:80573800-80574200	Enhancers	Hela-S3	cervix
14	chr16:80573800-80575000	Active TSS	Psoas Muscle	Psoas
15	chr16:80573800-80575000	Active TSS	Thymus	Thymus
16	chr16:80573800-80575400	Active TSS	Rectal Mucosa Donor 29	rectum

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