Variant report

Variant	rs17565505
Chromosome Location	chr5:152064433-152064434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10515675	0.83[EUR][1000 genomes]
rs10515676	0.83[EUR][1000 genomes]
rs11167584	0.83[EUR][1000 genomes]
rs11167589	0.88[ASN][1000 genomes]
rs11956651	0.83[EUR][1000 genomes]
rs13359939	0.83[EUR][1000 genomes]
rs17453481	0.81[EUR][1000 genomes]
rs17453530	0.81[EUR][1000 genomes]
rs17453740	0.81[EUR][1000 genomes]
rs17453775	0.81[EUR][1000 genomes]
rs17454420	0.85[EUR][1000 genomes]
rs17455800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550343	0.81[EUR][1000 genomes]
rs17565365	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17565470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17565693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565727	1.00[AFR][1000 genomes]
rs17565839	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3890802	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4246033	0.83[EUR][1000 genomes]
rs4398624	0.83[EUR][1000 genomes]
rs4406125	0.83[EUR][1000 genomes]
rs4484412	0.83[EUR][1000 genomes]
rs4484413	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4557395	0.81[EUR][1000 genomes]
rs4958320	0.81[EUR][1000 genomes]
rs4958323	0.85[EUR][1000 genomes]
rs4958562	0.81[EUR][1000 genomes]
rs4958564	0.85[EUR][1000 genomes]
rs4958566	0.83[EUR][1000 genomes]
rs4958567	0.83[EUR][1000 genomes]
rs4958568	0.82[EUR][1000 genomes]
rs4958569	0.82[EUR][1000 genomes]
rs4958573	1.00[AFR][1000 genomes]
rs4958574	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55648729	0.85[EUR][1000 genomes]
rs55786399	0.81[EUR][1000 genomes]
rs56014830	0.85[EUR][1000 genomes]
rs56047721	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs67979431	0.82[EUR][1000 genomes]
rs6871699	0.83[EUR][1000 genomes]
rs6884556	0.83[EUR][1000 genomes]
rs6895969	0.83[EUR][1000 genomes]
rs72795389	0.81[EUR][1000 genomes]
rs72797233	0.82[EUR][1000 genomes]
rs72797237	0.82[EUR][1000 genomes]
rs72797241	0.82[EUR][1000 genomes]
rs72797243	0.84[EUR][1000 genomes]
rs72797251	0.84[EUR][1000 genomes]
rs72797254	0.83[EUR][1000 genomes]
rs72797262	0.85[EUR][1000 genomes]
rs72797296	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72799113	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72799126	1.00[AFR][1000 genomes]
rs72799142	0.83[AFR][1000 genomes]
rs72799143	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72799145	0.88[ASN][1000 genomes]
rs72799172	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72799173	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72799176	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9324734	0.83[EUR][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
rs17565505	SLC26A2	cis	cerebellum	SCAN
rs17565505	GLRA1	cis	cerebellum	SCAN
rs17565505	IL17B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152063200-152068600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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