Variant report

Variant	rs9862718
Chromosome Location	chr3:54424701-54424702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12632768	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs13327362	0.91[CHD][hapmap]
rs13327625	0.87[EUR][1000 genomes]
rs1449326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1449327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449328	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449330	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449333	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1473345	0.99[ASN][1000 genomes]
rs1473346	0.99[ASN][1000 genomes]
rs1473347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1530733	0.87[CHD][hapmap]
rs1868497	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868500	0.91[CHD][hapmap]
rs1868502	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1868506	0.95[EUR][1000 genomes]
rs1868507	0.95[EUR][1000 genomes]
rs1868508	0.86[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs1975611	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1992963	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs1992964	0.83[ASW][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs2359789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs2359790	0.86[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2359792	0.87[EUR][1000 genomes]
rs2359793	0.86[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs4025912	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs4974360	0.87[CHD][hapmap]
rs4974370	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap]
rs6445653	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs731507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7372444	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7372695	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645545	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs7648293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9311528	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9311529	0.94[JPT][hapmap]
rs9827201	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs9830682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9841979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9851130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs9855860	1.00[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs9861155	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9862712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864105	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs9870407	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9877455	0.86[EUR][1000 genomes]
rs9877529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9882299	0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9862718	SEMA3G	cis	parietal	SCAN
rs9862718	TKT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54424600-54427200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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