Variant report

Variant	rs4997771
Chromosome Location	chr16:81905409-81905410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81829706..81831905-chr16:81903990..81906262,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10871423	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11150420	0.84[ASN][1000 genomes]
rs11150421	0.88[ASN][1000 genomes]
rs12102309	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445580	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12716921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716922	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12918486	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13330054	0.83[ASN][1000 genomes]
rs3934985	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935876	0.80[ASN][1000 genomes]
rs4243218	0.87[CHB][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs4499225	0.92[ASN][1000 genomes]
rs4889420	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889421	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs4997770	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997772	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997773	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997775	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55822905	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873405	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56215311	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7184247	0.87[CHB][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs7187163	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187837	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189106	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7189462	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7189843	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs7192509	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193967	0.83[ASN][1000 genomes]
rs7195281	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7196410	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7197677	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7197685	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197689	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197832	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7198813	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199941	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200324	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200626	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7200783	0.89[ASN][1000 genomes]
rs7202250	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72837428	0.97[ASN][1000 genomes]
rs72837429	0.97[ASN][1000 genomes]
rs7342694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8058099	0.81[ASN][1000 genomes]
rs8058287	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8058290	0.89[ASN][1000 genomes]
rs9923780	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924101	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9932716	0.81[LWK][hapmap];0.81[YRI][hapmap]

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	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
2	nsv573365	chr16:81804972-81975892	Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1065088	chr16:81878481-81953248	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv14137	chr16:81904767-81909407	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4997771	VAT1L	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81876200-81918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:81880000-81911200	Weak transcription	Pancreas	Pancrea
3	chr16:81880400-81908200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:81894800-81912400	Weak transcription	Fetal Intestine Small	intestine
5	chr16:81896800-81910400	Weak transcription	Gastric	stomach
6	chr16:81898800-81907400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr16:81898800-81912400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr16:81899000-81934600	Weak transcription	Right Atrium	heart
9	chr16:81900800-81925000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:81901000-81907800	Weak transcription	Liver	Liver
11	chr16:81901000-81929200	Weak transcription	Brain Substantia Nigra	brain
12	chr16:81901200-81911200	Weak transcription	Lung	lung
13	chr16:81901200-81925000	Weak transcription	Adipose Nuclei	Adipose
14	chr16:81901400-81906400	Weak transcription	HUVEC	blood vessel
15	chr16:81901400-81906600	Weak transcription	Fetal Thymus	thymus
16	chr16:81901600-81906200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr16:81901600-81906800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:81901800-81906600	Strong transcription	Primary hematopoietic stem cells	blood
19	chr16:81902000-81906200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr16:81902600-81906200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:81902600-81906200	Strong transcription	GM12878-XiMat	blood
22	chr16:81902600-81906400	Strong transcription	Primary B cells from cord blood	blood
23	chr16:81902600-81908000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr16:81902800-81955600	Weak transcription	Fetal Kidney	kidney
25	chr16:81903200-81907400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr16:81903200-81910000	Weak transcription	Spleen	Spleen
27	chr16:81904400-81906200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:81904400-81916800	Weak transcription	Fetal Intestine Large	intestine
29	chr16:81904800-81906200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr16:81905000-81907200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:81905200-81906000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr16:81905200-81906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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