Variant report

Variant	rs9866078
Chromosome Location	chr3:53635442-53635443
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:12)

rs_ID	r²[population]
rs1599230	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3774469	0.84[JPT][hapmap]
rs3774472	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774481	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes]
rs3821851	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6445590	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6803904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936450	0.81[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9810888	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]
rs9846874	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850569	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9859951	0.88[JPT][hapmap];0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9866078	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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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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