Variant report

Variant	rs2252089
Chromosome Location	chr1:217266729-217266730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1166347	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1166350	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1166351	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs1318282	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502357	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789579	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61066191	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6656214	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6682972	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs830310	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905292	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252089	VASH2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217264000-217271800	Weak transcription	Pancreas	Pancrea
2	chr1:217264200-217267200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:217264400-217269000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:217264400-217270800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:217265000-217267800	Weak transcription	Fetal Brain Male	brain
6	chr1:217265000-217269800	Weak transcription	Psoas Muscle	Psoas
7	chr1:217265200-217269000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:217265200-217269600	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:217265600-217269600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:217266200-217269800	Weak transcription	Right Ventricle	heart
11	chr1:217266200-217271200	Weak transcription	Fetal Heart	heart
12	chr1:217266200-217271400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:217266200-217271800	Weak transcription	Fetal Intestine Large	intestine

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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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