Variant report

Variant	rs9827591
Chromosome Location	chr3:60858696-60858697
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10048949	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10510855	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap]
rs13067776	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13071895	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13075102	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13078972	1.00[CEU][hapmap]
rs1447913	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1447914	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1947159	1.00[CEU][hapmap]
rs1947160	0.94[CEU][hapmap]
rs2223084	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs2736751	0.92[TSI][hapmap]
rs2736752	0.86[TSI][hapmap]
rs34412028	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34686536	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34700535	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35744933	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4974235	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs67192280	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67231683	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6765028	0.82[TSI][hapmap]
rs6766713	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6769544	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6772360	0.92[EUR][1000 genomes]
rs6772719	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6772800	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6780515	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6783370	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6785030	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785032	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6785095	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6785140	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs6787793	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6787911	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6788110	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6791272	0.94[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6793095	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs6793385	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6793580	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795855	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6796455	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6803394	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6804167	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73097803	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7613542	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap]
rs7622729	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7627303	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7636351	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7643970	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644380	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7646851	0.82[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7649286	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9754605	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9755687	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9758127	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9834435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9849318	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9849474	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9849492	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9869424	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870639	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9870642	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9870929	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534038	chr3:60781917-60993082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757872	chr3:60781943-61019003	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9827591	DNAH12	cis	parietal	SCAN
rs9827591	ACOX2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60855200-60862800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:60858600-60859000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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