Variant report

Variant	rs12509742
Chromosome Location	chr4:62645032-62645033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10000772	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10006513	0.93[EUR][1000 genomes]
rs10015258	0.95[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs10017044	0.90[EUR][1000 genomes]
rs1031341	0.93[EUR][1000 genomes]
rs11734607	0.90[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1376306	0.93[EUR][1000 genomes]
rs1376307	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1450901	0.93[EUR][1000 genomes]
rs1470721	0.93[EUR][1000 genomes]
rs17090543	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1817052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868789	0.87[ASN][1000 genomes]
rs1868790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1901222	0.88[ASN][1000 genomes]
rs1901223	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013374	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2122640	1.00[CEU][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes]
rs2122641	0.87[ASN][1000 genomes]
rs2122642	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2122643	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2167280	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198056	0.89[ASN][1000 genomes]
rs2345041	0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2345043	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2345044	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2345045	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2345046	0.99[EUR][1000 genomes]
rs2345047	1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2345048	0.82[EUR][1000 genomes]
rs2345049	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs28534995	0.89[ASN][1000 genomes]
rs28735546	0.96[EUR][1000 genomes]
rs2881027	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28861113	0.92[EUR][1000 genomes]
rs34637663	0.88[ASN][1000 genomes]
rs34907045	0.89[ASN][1000 genomes]
rs35946366	0.88[ASN][1000 genomes]
rs4467601	0.86[ASN][1000 genomes]
rs4487384	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4493573	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4495065	0.82[ASW][hapmap]
rs4860104	0.93[EUR][1000 genomes]
rs4860434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860435	0.93[EUR][1000 genomes]
rs62304373	0.89[ASN][1000 genomes]
rs6551658	0.88[ASN][1000 genomes]
rs6818785	0.93[EUR][1000 genomes]
rs6843246	0.82[ASW][hapmap]
rs6845019	0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6855424	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7656882	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7676289	1.00[ASN][1000 genomes]
rs7679793	0.89[ASN][1000 genomes]
rs969965	0.93[EUR][1000 genomes]
rs9790538	0.88[ASN][1000 genomes]
rs9884313	0.87[ASN][1000 genomes]
rs990640	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9942184	0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][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	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv829949	chr4:62615637-62761629	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62637600-62656000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:62641000-62654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:62641200-62645600	Weak transcription	Fetal Brain Male	brain
4	chr4:62641400-62645800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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