Variant report

Variant	rs11239417
Chromosome Location	chr10:45787725-45787726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10159580	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10508894	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793613	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10900195	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10900197	1.00[YRI][hapmap]
rs10900200	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10900209	1.00[ASN][1000 genomes]
rs11239398	1.00[ASN][1000 genomes]
rs11239402	0.89[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239409	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239420	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239422	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239423	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11239426	0.82[AFR][1000 genomes]
rs11239427	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239428	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239429	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239430	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239432	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11239433	0.81[AFR][1000 genomes]
rs11239434	1.00[ASN][1000 genomes]
rs11239435	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11239437	1.00[ASN][1000 genomes]
rs11239452	1.00[ASN][1000 genomes]
rs11239480	1.00[ASN][1000 genomes]
rs11239482	1.00[ASN][1000 genomes]
rs11239496	1.00[ASN][1000 genomes]
rs11239501	1.00[ASN][1000 genomes]
rs11239506	1.00[ASN][1000 genomes]
rs11239512	1.00[ASN][1000 genomes]
rs11239515	1.00[ASN][1000 genomes]
rs11239516	1.00[ASN][1000 genomes]
rs11239517	1.00[ASN][1000 genomes]
rs11239519	1.00[ASN][1000 genomes]
rs11239520	1.00[ASN][1000 genomes]
rs11511611	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11522530	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11522531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11522532	1.00[ASN][1000 genomes]
rs11523406	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523407	1.00[ASN][1000 genomes]
rs11523864	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523866	1.00[ASN][1000 genomes]
rs12146275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246128	0.85[AFR][1000 genomes]
rs12250005	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12256027	1.00[ASN][1000 genomes]
rs12268890	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12355274	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357069	1.00[ASN][1000 genomes]
rs12358110	1.00[ASN][1000 genomes]
rs12358817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359547	1.00[ASN][1000 genomes]
rs12359672	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529828	1.00[ASN][1000 genomes]
rs1529829	1.00[ASN][1000 genomes]
rs17157583	1.00[ASN][1000 genomes]
rs17157619	1.00[ASN][1000 genomes]
rs17157680	0.82[AFR][1000 genomes]
rs17157697	1.00[YRI][hapmap]
rs17157699	0.89[YRI][hapmap]
rs17443340	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444064	1.00[ASN][1000 genomes]
rs17520779	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17521948	1.00[ASN][1000 genomes]
rs1815626	1.00[ASN][1000 genomes]
rs1968475	1.00[ASN][1000 genomes]
rs28485654	1.00[ASN][1000 genomes]
rs28688874	1.00[ASN][1000 genomes]
rs2871740	1.00[ASN][1000 genomes]
rs41526545	1.00[ASN][1000 genomes]
rs55963543	1.00[ASN][1000 genomes]
rs57580056	0.81[AFR][1000 genomes]
rs6593484	1.00[ASN][1000 genomes]
rs7079686	0.82[AFR][1000 genomes]
rs7085353	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7098434	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098888	1.00[ASN][1000 genomes]
rs72784518	1.00[ASN][1000 genomes]
rs72784536	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784538	1.00[ASN][1000 genomes]
rs72784571	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786508	1.00[ASN][1000 genomes]
rs72788095	1.00[ASN][1000 genomes]
rs72788096	1.00[ASN][1000 genomes]
rs72788101	1.00[ASN][1000 genomes]
rs72788102	1.00[ASN][1000 genomes]
rs72789705	1.00[ASN][1000 genomes]
rs72789735	1.00[ASN][1000 genomes]
rs748126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748127	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898796	1.00[ASN][1000 genomes]
rs7907779	1.00[ASN][1000 genomes]
rs9664826	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9731035	1.00[ASN][1000 genomes]
rs9733175	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9733422	1.00[ASN][1000 genomes]
rs9733444	0.94[AFR][1000 genomes];1.00[ASN][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	esv2750897	chr10:45550145-45820136	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv895105	chr10:45636867-45928822	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11239417	ALOX5	cis	cerebellum	SCAN
rs11239417	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs11239417	ALOX5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45786000-45790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:45787200-45789000	Enhancers	Brain Substantia Nigra	brain
3	chr10:45787400-45787800	Enhancers	Brain Angular Gyrus	brain

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