Variant report

Variant	rs6593482
Chromosome Location	chr10:45868449-45868450
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCLAF1	chr10:45868399-45868908	GM12878	blood:	n/a	chr10:45868718-45868727
2	POLR2A	chr10:45867707-45870526	Raji	blood:	n/a	n/a
3	POLR2A	chr10:45868366-45869926	GM12891	blood:	n/a	n/a
4	EP300	chr10:45868359-45868450	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:45868312-45869887	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
ALOX5	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10900212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239486	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11239491	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239492	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239497	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239505	0.93[ASN][1000 genomes]
rs11511619	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11511620	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11517281	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11523408	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354712	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12354742	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12354994	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12356109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356140	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12358647	0.91[ASN][1000 genomes]
rs12359299	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12359302	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12360250	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12762303	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12763738	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12764778	0.99[ASN][1000 genomes]
rs12768010	0.98[ASN][1000 genomes]
rs12774369	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12783095	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12783182	0.90[ASN][1000 genomes]
rs12783895	0.80[ASN][1000 genomes]
rs17157728	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17157733	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17157736	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864412	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864413	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864414	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082108	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099170	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303885	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2310776	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28395865	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34297550	0.90[ASN][1000 genomes]
rs34462692	0.87[ASN][1000 genomes]
rs34929604	0.80[ASN][1000 genomes]
rs34998367	0.90[ASN][1000 genomes]
rs35001574	0.88[ASN][1000 genomes]
rs35267934	0.90[ASN][1000 genomes]
rs35300270	0.81[ASN][1000 genomes]
rs35536930	0.81[ASN][1000 genomes]
rs35555369	0.83[ASN][1000 genomes]
rs35906360	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3780894	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780896	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780897	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780898	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780899	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3824613	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4986832	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987105	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987106	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55717607	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55787481	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55864145	0.98[ASN][1000 genomes]
rs55965812	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55978138	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55986122	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56150414	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56180358	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57063108	0.99[ASN][1000 genomes]
rs57398542	0.89[ASN][1000 genomes]
rs58167894	0.81[ASN][1000 genomes]
rs58238740	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58901177	0.99[ASN][1000 genomes]
rs59514896	0.81[ASN][1000 genomes]
rs60146827	0.81[ASN][1000 genomes]
rs60842538	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6413416	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593478	0.86[ASN][1000 genomes]
rs66489870	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67008983	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67491417	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7071714	0.90[ASN][1000 genomes]
rs7077891	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7080897	0.81[ASN][1000 genomes]
rs7081004	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7083500	0.85[ASN][1000 genomes]
rs7084793	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085205	0.85[ASN][1000 genomes]
rs7093687	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097429	0.81[ASN][1000 genomes]
rs71494771	0.81[ASN][1000 genomes]
rs71494772	0.86[ASN][1000 genomes]
rs71494775	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71494776	0.92[ASN][1000 genomes]
rs71494779	0.81[ASN][1000 genomes]
rs72561472	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs745986	0.93[ASN][1000 genomes]
rs7896861	0.90[ASN][1000 genomes]
rs7898465	0.90[ASN][1000 genomes]
rs7909740	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909768	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913488	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917687	0.81[ASN][1000 genomes]
rs7918542	0.81[ASN][1000 genomes]
rs7919239	0.82[ASN][1000 genomes]
rs7921503	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663661	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	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
4	nsv895107	chr10:45850300-45953767	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6593482	ALOX5	cis	lymphoblastoid	seeQTL
rs6593482	ALOX5	cis	parietal	SCAN
rs6593482	ALOX5	cis	cerebellum	SCAN
rs6593482	OR13A1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45867400-45870200	Active TSS	GM12878-XiMat	blood
2	chr10:45868000-45868600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:45868000-45868600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
4	chr10:45868000-45869400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr10:45868200-45868600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr10:45868200-45868600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr10:45868200-45868600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:45868200-45868800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr10:45868200-45870600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr10:45868400-45868600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr10:45868400-45868600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
12	chr10:45868400-45868600	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
13	chr10:45868400-45868600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr10:45868400-45868600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:45868400-45868600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:45868400-45868600	Enhancers	Adipose Nuclei	Adipose
17	chr10:45868400-45868600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr10:45868400-45868600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
19	chr10:45868400-45868600	Bivalent Enhancer	Fetal Kidney	kidney
20	chr10:45868400-45868800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr10:45868400-45868800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
22	chr10:45868400-45868800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:45868400-45868800	Flanking Active TSS	K562	blood
24	chr10:45868400-45869000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:45868400-45869400	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr10:45868400-45869800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr10:45868400-45870000	Active TSS	Thymus	Thymus
28	chr10:45868400-45870200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr10:45868400-45870200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr10:45868400-45870200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr10:45868400-45870400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr10:45868400-45870400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:45868400-45870600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr10:45868400-45871000	Active TSS	Brain Substantia Nigra	brain

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