Variant report

Variant	rs12359547
Chromosome Location	chr10:45849953-45849954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10159580	0.89[CEU][hapmap];1.00[CHB][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	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs10900200	0.89[CEU][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	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11239437	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239452	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[CHB][hapmap];1.00[ASN][1000 genomes]
rs11239506	1.00[ASN][1000 genomes]
rs11239512	1.00[ASN][1000 genomes]
rs11239515	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11239516	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11239517	1.00[ASN][1000 genomes]
rs11239519	1.00[ASN][1000 genomes]
rs11239520	1.00[ASN][1000 genomes]
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]
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	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17443340	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444064	1.00[CHB][hapmap];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	0.89[CEU][hapmap];1.00[CHB][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12359547	OR13A1	cis	lung	GTEx
rs12359547	ALOX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 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	chr10:45848800-45850400	Enhancers	K562	blood
7	chr10:45848800-45851400	Weak transcription	Esophagus	oesophagus
8	chr10:45849000-45850000	Weak transcription	Adipose Nuclei	Adipose
9	chr10:45849800-45850200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:45849800-45850600	Enhancers	Placenta	Placenta
11	chr10:45849800-45850600	Enhancers	Osteobl	bone
12	chr10:45849800-45852000	Enhancers	GM12878-XiMat	blood

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