Variant report

Variant	rs9810888
Chromosome Location	chr3:53635595-53635596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1599230	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774472	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774475	0.83[ASN][1000 genomes]
rs3774481	0.95[CHB][hapmap]
rs6445590	0.95[CHB][hapmap]
rs6803904	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9846874	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9850569	0.95[CHB][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs9866078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Systolic blood pressure	25249183	GWAS catalog
Diastolic blood pressure	25249183	GWAS catalog
Hypertension	25249183	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9810888	AMIGO3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53605800-53645200	Weak transcription	Pancreas	Pancrea
2	chr3:53623600-53637200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:53631800-53636800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:53632200-53639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53632200-53640400	Weak transcription	Fetal Lung	lung
6	chr3:53633600-53635800	Strong transcription	Fetal Intestine Large	intestine
7	chr3:53635200-53645200	Weak transcription	Lung	lung
8	chr3:53635400-53650200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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

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