Variant report

Variant	rs4958573
Chromosome Location	chr5:152091739-152091740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11167589	0.88[EUR][1000 genomes]
rs11167597	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153328	1.00[ASN][1000 genomes]
rs12188960	1.00[ASN][1000 genomes]
rs17455800	1.00[AFR][1000 genomes]
rs17488630	1.00[ASN][1000 genomes]
rs17565365	1.00[AFR][1000 genomes]
rs17565470	1.00[AFR][1000 genomes]
rs17565505	1.00[AFR][1000 genomes]
rs17565693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17565727	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565839	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3890802	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4484413	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4958574	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55992747	1.00[ASN][1000 genomes]
rs56047721	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72799113	1.00[AFR][1000 genomes]
rs72799126	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799142	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799143	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72799172	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72799173	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72799176	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72799185	1.00[ASN][1000 genomes]
rs72802868	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription 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	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4958573	IL17B	cis	parietal	SCAN
rs4958573	GLRA1	cis	cerebellum	SCAN
rs4958573	SLC26A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152091400-152091800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:152091600-152092000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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