Variant report

Variant	rs2359793
Chromosome Location	chr3:54406659-54406660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12632768	0.80[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs13327625	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449326	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs1449327	0.84[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1449328	0.89[EUR][1000 genomes]
rs1449329	0.86[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs1449330	0.81[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs1473345	0.84[EUR][1000 genomes]
rs1473346	0.84[EUR][1000 genomes]
rs1473347	0.85[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs1473348	0.85[GIH][hapmap];0.82[TSI][hapmap]
rs1868497	0.89[EUR][1000 genomes]
rs1868502	0.81[EUR][1000 genomes]
rs1868506	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868507	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975611	0.83[EUR][1000 genomes]
rs1992963	0.89[GIH][hapmap]
rs1992964	0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs2359789	0.85[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs2359790	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2359792	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4025912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4131315	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs4974369	0.83[JPT][hapmap]
rs4974370	0.80[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs6804196	0.82[GIH][hapmap]
rs731507	0.83[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs731508	0.82[GIH][hapmap]
rs7372444	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7372695	0.81[EUR][1000 genomes]
rs7429237	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs7431094	0.83[EUR][1000 genomes]
rs7648293	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs7653648	0.82[TSI][hapmap]
rs9311529	0.81[MEX][hapmap]
rs9817603	0.82[GIH][hapmap]
rs9827201	1.00[CEU][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830682	0.86[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9836159	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs9841318	0.83[JPT][hapmap]
rs9843412	0.82[GIH][hapmap]
rs9851130	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9862712	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs9862718	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs9870407	0.85[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9877288	0.89[EUR][1000 genomes]
rs9877455	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9877529	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs9882299	0.86[JPT][hapmap]

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	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
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2359793	RBM15B	cis	cerebellum	SCAN
rs2359793	TKT	cis	parietal	SCAN
rs2359793	SEMA3G	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54392600-54410200	Weak transcription	Ovary	ovary
2	chr3:54395400-54407800	Weak transcription	Hela-S3	cervix
3	chr3:54395400-54409000	Weak transcription	Right Atrium	heart
4	chr3:54401000-54409600	Weak transcription	Fetal Lung	lung
5	chr3:54406400-54410200	Weak transcription	Psoas Muscle	Psoas

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