Variant report

Variant	rs1402716
Chromosome Location	chr2:212882926-212882927
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10169217	0.87[ASN][1000 genomes]
rs10197270	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10445808	1.00[CHB][hapmap]
rs10497958	1.00[CHB][hapmap]
rs12373751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12464843	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12466520	1.00[ASN][1000 genomes]
rs12470737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12473708	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12476163	1.00[CHB][hapmap]
rs12476274	0.81[ASN][1000 genomes]
rs12477159	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12478950	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12994785	0.83[YRI][hapmap]
rs1402718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464443	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1473636	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1473637	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473638	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521537	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1521550	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1521553	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1546717	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16847568	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16847575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16847580	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17337014	0.85[JPT][hapmap]
rs17343912	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17343932	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17344051	1.00[CHD][hapmap]
rs17344065	1.00[CHB][hapmap]
rs17415843	0.83[ASN][1000 genomes]
rs17415969	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17416172	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1879637	0.85[JPT][hapmap]
rs2139939	1.00[CHB][hapmap]
rs2139940	1.00[CHB][hapmap]
rs2371444	1.00[CHB][hapmap]
rs4672634	1.00[CHB][hapmap]
rs4672636	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs59081924	0.90[ASN][1000 genomes]
rs6435684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435691	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6712126	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6715981	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087372	0.94[ASN][1000 genomes]
rs7574462	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7582903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7595560	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs939645	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs960824	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9678219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875792	chr2:212824999-212896571	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv584343	chr2:212830200-212906355	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1012269	chr2:212837487-212915640	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv525127	chr2:212839046-212916758	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1011572	chr2:212840066-213152279	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875794	chr2:212842777-212885510	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
7	nsv875797	chr2:212847605-212888988	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
8	nsv875798	chr2:212852669-212961992	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv875800	chr2:212856539-212896571	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv875801	chr2:212856539-212929014	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv460071	chr2:212860841-212888988	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	nsv584344	chr2:212860841-212888988	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv460072	chr2:212864338-212891401	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv584345	chr2:212864338-212891401	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv875802	chr2:212867291-213004603	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv875803	chr2:212874828-212969560	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402716	VWC2L	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212880200-212883800	Enhancers	Osteobl	bone
2	chr2:212881000-212884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:212881200-212883600	Weak transcription	Fetal Heart	heart
4	chr2:212881600-212883000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:212882200-212883200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:212882400-212883600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:212882800-212892000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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