Variant report

Variant	rs11239435
Chromosome Location	chr10:45802840-45802841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10159580	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508894	1.00[ASN][1000 genomes]
rs10793613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900197	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10900200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900209	0.89[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	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11239420	1.00[ASN][1000 genomes]
rs11239422	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11239423	1.00[ASN][1000 genomes]
rs11239424	0.96[AFR][1000 genomes]
rs11239426	0.84[AFR][1000 genomes]
rs11239427	1.00[ASN][1000 genomes]
rs11239428	1.00[ASN][1000 genomes]
rs11239429	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11239430	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239433	0.85[AFR][1000 genomes]
rs11239434	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239436	1.00[CEU][hapmap]
rs11239437	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239452	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239480	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239482	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239496	0.90[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]
rs11511611	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11522530	1.00[ASN][1000 genomes]
rs11522531	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11522532	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523406	1.00[ASN][1000 genomes]
rs11523407	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523864	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11523866	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146275	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12246128	0.81[AFR][1000 genomes]
rs12250005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256027	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268890	0.89[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355274	1.00[ASN][1000 genomes]
rs12355722	0.87[EUR][1000 genomes]
rs12357069	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358110	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358817	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12359547	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359672	1.00[ASN][1000 genomes]
rs12360419	0.81[EUR][1000 genomes]
rs1529828	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529829	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157583	1.00[ASN][1000 genomes]
rs17157619	1.00[ASN][1000 genomes]
rs17157680	0.85[AFR][1000 genomes]
rs17157697	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17157699	0.89[YRI][hapmap]
rs17443340	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444064	1.00[ASN][1000 genomes]
rs17520779	1.00[ASN][1000 genomes]
rs17521948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815626	1.00[ASN][1000 genomes]
rs1968475	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485654	1.00[ASN][1000 genomes]
rs28570111	0.97[EUR][1000 genomes]
rs28688874	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871740	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41526545	1.00[ASN][1000 genomes]
rs55963543	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57580056	0.85[AFR][1000 genomes]
rs6593484	1.00[ASN][1000 genomes]
rs7079686	0.84[AFR][1000 genomes]
rs7085353	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098434	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];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	0.92[EUR][1000 genomes]
rs72786508	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788095	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788096	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788101	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788102	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789705	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789735	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748126	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs748127	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7898796	1.00[ASN][1000 genomes]
rs7907779	1.00[ASN][1000 genomes]
rs9664826	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9731035	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9733175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9733422	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9733444	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11239435	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs11239435	ALOX5	cis	cerebellum	SCAN
rs11239435	ALOX5	cis	parietal	SCAN
rs11239435	OR13A1	cis	cerebellum	SCAN
rs11239435	ALOX5	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45798600-45803800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:45798600-45804000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:45801200-45804600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr10:45802200-45803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr10:45802400-45803200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr10:45802400-45803200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr10:45802400-45803200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr10:45802400-45803200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr10:45802400-45803800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr10:45802400-45804000	Weak transcription	K562	blood
11	chr10:45802400-45804400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr10:45802600-45803200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:45802800-45803000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr10:45802800-45804200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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