Variant report

Variant	rs17565365
Chromosome Location	chr5:152056234-152056235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10155517	0.95[ASN][1000 genomes]
rs10515675	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10515676	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11167584	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956651	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13359939	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361438	0.91[ASN][1000 genomes]
rs17452991	0.95[ASN][1000 genomes]
rs17453481	0.84[EUR][1000 genomes]
rs17453530	0.84[EUR][1000 genomes]
rs17453740	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453775	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454420	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455800	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17550343	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565470	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17565505	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17565693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17565727	1.00[AFR][1000 genomes]
rs17565839	1.00[AFR][1000 genomes]
rs2961756	0.95[ASN][1000 genomes]
rs2961760	0.95[ASN][1000 genomes]
rs2961765	0.95[ASN][1000 genomes]
rs2961766	0.90[ASN][1000 genomes]
rs2964230	0.95[ASN][1000 genomes]
rs2964231	0.95[ASN][1000 genomes]
rs3890802	1.00[AFR][1000 genomes]
rs3923209	0.95[ASN][1000 genomes]
rs4246033	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398624	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4406125	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4478308	0.95[ASN][1000 genomes]
rs4484412	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4484413	0.83[AFR][1000 genomes]
rs4557395	0.84[EUR][1000 genomes]
rs4580766	0.95[ASN][1000 genomes]
rs4958316	0.95[ASN][1000 genomes]
rs4958317	0.95[ASN][1000 genomes]
rs4958320	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958323	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958560	0.95[ASN][1000 genomes]
rs4958561	0.95[ASN][1000 genomes]
rs4958562	0.84[EUR][1000 genomes]
rs4958564	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958566	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958567	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4958568	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958569	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958573	1.00[AFR][1000 genomes]
rs4958574	1.00[AFR][1000 genomes]
rs55648729	0.87[EUR][1000 genomes]
rs55786399	0.84[EUR][1000 genomes]
rs56014830	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047721	0.83[AFR][1000 genomes]
rs67979431	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871699	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6876403	0.83[ASN][1000 genomes]
rs6876723	0.95[ASN][1000 genomes]
rs6884556	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6895969	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72795376	0.95[ASN][1000 genomes]
rs72795379	0.95[ASN][1000 genomes]
rs72795389	0.84[EUR][1000 genomes]
rs72797226	1.00[ASN][1000 genomes]
rs72797233	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797237	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797241	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797243	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797251	0.87[EUR][1000 genomes]
rs72797254	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72797262	0.87[EUR][1000 genomes]
rs72797296	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799126	1.00[AFR][1000 genomes]
rs72799142	0.83[AFR][1000 genomes]
rs72799143	0.83[AFR][1000 genomes]
rs72799172	0.83[AFR][1000 genomes]
rs72799173	0.83[AFR][1000 genomes]
rs72799176	0.83[AFR][1000 genomes]
rs9324734	0.86[EUR][1000 genomes];0.91[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
rs17565365	IL17B	cis	parietal	SCAN
rs17565365	GLRA1	cis	cerebellum	SCAN
rs17565365	SLC26A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152055600-152056800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:152056200-152056400	Enhancers	Pancreatic Islets	Pancreatic Islet

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