Variant report

Variant	rs4709773
Chromosome Location	chr6:164275440-164275441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1028485	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1040641	0.83[ASN][1000 genomes]
rs10806784	0.87[EUR][1000 genomes]
rs1111705	0.83[ASN][1000 genomes]
rs13203619	0.93[ASN][1000 genomes]
rs1555229	0.81[CHB][hapmap]
rs2015261	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321978	0.80[CHB][hapmap]
rs4709760	0.83[ASN][1000 genomes]
rs4709765	0.83[ASN][1000 genomes]
rs4709766	0.83[ASN][1000 genomes]
rs4709775	0.87[EUR][1000 genomes]
rs8180622	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs880095	0.85[ASN][1000 genomes]
rs9295231	0.82[ASN][1000 genomes]
rs9295232	0.85[ASN][1000 genomes]
rs9295233	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9346974	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9346975	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9347791	0.82[ASN][1000 genomes]
rs9347792	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9347793	0.83[ASN][1000 genomes]
rs9347798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347799	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9355439	0.83[ASN][1000 genomes]
rs9355440	0.85[ASN][1000 genomes]
rs9355442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9356156	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356159	0.86[EUR][1000 genomes]
rs9356160	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9364703	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9365619	0.85[ASN][1000 genomes]
rs9365620	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9365624	0.86[EUR][1000 genomes]
rs9365625	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9456885	0.83[ASN][1000 genomes]
rs9458911	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1798922	chr6:164257563-164298780	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4709773	NCRNA00241	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164273600-164276200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:164274800-164275600	Enhancers	K562	blood
3	chr6:164275400-164275600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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