Variant report

Variant	rs11239480
Chromosome Location	chr10:45849370-45849371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10159580	0.91[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508894	1.00[ASN][1000 genomes]
rs10793613	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900195	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900197	0.91[CEU][hapmap]
rs10900200	0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900209	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239398	1.00[ASN][1000 genomes]
rs11239402	1.00[ASN][1000 genomes]
rs11239409	1.00[ASN][1000 genomes]
rs11239417	1.00[ASN][1000 genomes]
rs11239420	1.00[ASN][1000 genomes]
rs11239422	1.00[ASN][1000 genomes]
rs11239423	1.00[ASN][1000 genomes]
rs11239427	1.00[ASN][1000 genomes]
rs11239428	1.00[ASN][1000 genomes]
rs11239429	1.00[ASN][1000 genomes]
rs11239430	1.00[ASN][1000 genomes]
rs11239432	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239434	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239435	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239436	0.90[CEU][hapmap]
rs11239437	0.91[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239452	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239496	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];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]
rs11239523	0.85[MEX][hapmap]
rs11511611	1.00[ASN][1000 genomes]
rs11522530	1.00[ASN][1000 genomes]
rs11522531	1.00[ASN][1000 genomes]
rs11522532	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523406	1.00[ASN][1000 genomes]
rs11523407	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523864	1.00[ASN][1000 genomes]
rs11523866	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146275	1.00[ASN][1000 genomes]
rs12250005	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256027	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268890	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355274	1.00[ASN][1000 genomes]
rs12357069	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358110	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358817	1.00[ASN][1000 genomes]
rs12359547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359672	1.00[ASN][1000 genomes]
rs1529828	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529829	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157583	1.00[ASN][1000 genomes]
rs17157619	1.00[ASN][1000 genomes]
rs17157697	0.91[CEU][hapmap]
rs17443340	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444064	1.00[ASN][1000 genomes]
rs17520779	1.00[ASN][1000 genomes]
rs17521948	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815626	1.00[ASN][1000 genomes]
rs1968475	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485654	1.00[ASN][1000 genomes]
rs28570111	0.90[EUR][1000 genomes]
rs28688874	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871740	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41526545	1.00[ASN][1000 genomes]
rs55963543	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593484	1.00[ASN][1000 genomes]
rs7085353	0.91[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098434	1.00[ASN][1000 genomes]
rs7098888	1.00[ASN][1000 genomes]
rs72784518	1.00[ASN][1000 genomes]
rs72784536	1.00[ASN][1000 genomes]
rs72784538	1.00[ASN][1000 genomes]
rs72784571	1.00[ASN][1000 genomes]
rs72784580	0.81[EUR][1000 genomes]
rs72786508	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788095	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788096	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789735	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748126	1.00[ASN][1000 genomes]
rs748127	1.00[ASN][1000 genomes]
rs7898796	1.00[ASN][1000 genomes]
rs7907779	1.00[ASN][1000 genomes]
rs9664826	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9731035	1.00[ASN][1000 genomes]
rs9733175	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9733422	1.00[ASN][1000 genomes]
rs9733444	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11239480	OR13A1	cis	cerebellum	SCAN
rs11239480	ALOX5	cis	lymphoblastoid	seeQTL
rs11239480	ALOX5	cis	cerebellum	SCAN
rs11239480	ALOX5	cis	parietal	SCAN
rs11239480	OR13A1	cis	lung	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45847400-45850000	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:45848200-45850200	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr10:45848200-45850400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:45848200-45850400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:45848400-45863400	Weak transcription	Primary B cells from cord blood	blood
6	chr10:45848800-45849400	Enhancers	GM12878-XiMat	blood
7	chr10:45848800-45850400	Enhancers	K562	blood
8	chr10:45848800-45851400	Weak transcription	Esophagus	oesophagus
9	chr10:45849000-45850000	Weak transcription	Adipose Nuclei	Adipose

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