Variant report

Variant	rs6687620
Chromosome Location	chr1:67648460-67648461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127763	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs10889665	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889667	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889668	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11208997	1.00[ASW][hapmap]
rs11801083	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321156	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs1358748	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358749	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884443	0.92[EUR][1000 genomes]
rs2064691	0.91[EUR][1000 genomes]
rs2180296	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2863203	0.95[EUR][1000 genomes]
rs4655521	0.87[EUR][1000 genomes]
rs4655522	0.87[EUR][1000 genomes]
rs4655681	0.93[EUR][1000 genomes]
rs4655688	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655689	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655690	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6666144	0.91[EUR][1000 genomes]
rs6683455	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684024	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687611	1.00[ASW][hapmap]
rs6703475	0.91[EUR][1000 genomes]
rs7518757	0.86[EUR][1000 genomes]
rs7531589	1.00[ASW][hapmap]
rs7540900	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]

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	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv461762	chr1:67551209-67648460	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv546446	chr1:67551209-67648460	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687620	WLS	cis	parietal	SCAN
rs6687620	IL23R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67648400-67648800	Active TSS	Brain Substantia Nigra	brain

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