Variant report

Variant	rs12587324
Chromosome Location	chr14:97380847-97380848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10873476	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10873477	0.91[EUR][1000 genomes]
rs11160375	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12880379	0.84[ASN][1000 genomes]
rs1385551	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1885162	0.83[ASN][1000 genomes]
rs2145642	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34459530	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4905568	0.81[AMR][1000 genomes]
rs61981034	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981037	0.87[EUR][1000 genomes]
rs749280	0.84[ASN][1000 genomes]
rs8019314	0.82[ASN][1000 genomes]
rs8019561	0.83[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	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948620	chr14:97334444-98133191	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv832867	chr14:97365919-97541763	Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12587324	VRK1	cis	parietal	SCAN
rs12587324	VRK1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97368600-97391400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:97376800-97387600	Weak transcription	Thymus	Thymus
3	chr14:97378400-97383000	Weak transcription	K562	blood
4	chr14:97379000-97387800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:97379400-97411800	Weak transcription	Primary T cells from cord blood	blood
6	chr14:97379800-97383000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr14:97380200-97381400	Enhancers	Fetal Brain Female	brain
8	chr14:97380200-97381400	Enhancers	Fetal Heart	heart
9	chr14:97380400-97381200	Enhancers	Fetal Brain Male	brain
10	chr14:97380600-97381200	Enhancers	Spleen	Spleen
11	chr14:97380600-97381200	Strong transcription	Dnd41	blood
12	chr14:97380800-97381200	Enhancers	Adipose Nuclei	Adipose
13	chr14:97380800-97381200	Weak transcription	Fetal Muscle Leg	muscle

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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