Variant report

Variant	rs7355411
Chromosome Location	chr2:56518623-56518624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10172020	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10175691	0.83[CHB][hapmap]
rs10200604	0.92[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs10203280	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs11125619	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs11125621	0.81[CEU][hapmap]
rs11125622	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs11886381	0.84[CHB][hapmap]
rs12463587	0.85[EUR][1000 genomes]
rs13384655	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389344	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13392111	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1549031	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17047781	0.85[CEU][hapmap]
rs17047791	0.86[EUR][1000 genomes]
rs17047802	0.85[CEU][hapmap]
rs17047851	0.92[CHB][hapmap]
rs17047854	0.92[CHB][hapmap]
rs17047856	0.84[CHB][hapmap]
rs17268785	0.92[CHB][hapmap]
rs4287805	0.86[LWK][hapmap];0.85[MKK][hapmap]
rs4671278	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs4672105	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672107	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672109	0.84[CEU][hapmap]
rs4672110	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6545572	0.92[CHB][hapmap]
rs6545574	0.89[CHB][hapmap]
rs6704684	0.92[CHB][hapmap]
rs6732270	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735003	0.92[CHB][hapmap]
rs6747380	0.91[CHB][hapmap]
rs6748308	0.92[CHB][hapmap]
rs6760269	0.92[CHB][hapmap]
rs72803024	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72803026	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7355401	0.92[AFR][1000 genomes]
rs7562381	0.92[CHB][hapmap]
rs7566597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530516	chr2:56447922-56633505	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv522006	chr2:56496589-56545845	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv874170	chr2:56496589-56590865	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7355411	VRK2	cis	cerebellum	SCAN
rs7355411	SPTBN1	cis	cerebellum	SCAN
rs7355411	RPL23AP32	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56515600-56526600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:56516400-56523400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:56516400-56525800	Weak transcription	HSMM	muscle
4	chr2:56516800-56524800	Weak transcription	Psoas Muscle	Psoas
5	chr2:56517200-56524800	Weak transcription	Left Ventricle	heart
6	chr2:56517400-56520000	Weak transcription	Adipose Nuclei	Adipose

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