Variant report

Variant	rs9463480
Chromosome Location	chr6:49400795-49400796
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49393144..49396120-chr6:49398943..49401576,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10456622	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141321	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196937	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209900	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212022	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086421	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147570	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448701	0.84[EUR][1000 genomes]
rs2448702	0.84[EUR][1000 genomes]
rs2448707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477405	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477406	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493440	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501961	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501962	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501977	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501979	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501980	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729619	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823114	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4348317	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458686	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469291	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4573082	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715129	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715131	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60982898	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411929	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411930	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411932	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458690	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458693	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458694	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901278	0.83[EUR][1000 genomes]
rs6909128	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923124	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744595	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769018	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296616	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463473	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463474	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463475	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463476	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463477	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463479	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463483	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473547	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473549	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473551	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473552	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473553	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473555	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473557	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473563	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473566	0.83[EUR][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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS 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
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9463480	CENPQ	cis	Nerve Tibial	GTEx
rs9463480	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9463480	MUT	cis	multi-tissue	Pritchard
rs9463480	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9463480	MUT	cis	Nerve Tibial	GTEx
rs9463480	CENPQ	cis	Thyroid	GTEx
rs9463480	CENPQ	cis	Artery Tibial	GTEx
rs9463480	CENPQ	cis	Esophagus Muscularis	GTEx
rs9463480	MUT	cis	Artery Tibial	GTEx
rs9463480	CENPQ	cis	lung	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49389600-49401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:49391000-49401200	Weak transcription	Left Ventricle	heart
3	chr6:49392400-49403800	Weak transcription	Right Ventricle	heart
4	chr6:49393400-49406400	Weak transcription	Lung	lung
5	chr6:49394800-49403200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:49395000-49402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:49395200-49406400	Weak transcription	Fetal Intestine Small	intestine
8	chr6:49395200-49406400	Weak transcription	Fetal Stomach	stomach
9	chr6:49395200-49406400	Weak transcription	Gastric	stomach
10	chr6:49395200-49406400	Weak transcription	Spleen	Spleen
11	chr6:49395400-49400800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:49395400-49400800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:49395400-49400800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:49395400-49402400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:49395400-49406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:49395600-49400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:49395600-49403200	Weak transcription	Psoas Muscle	Psoas
19	chr6:49395600-49406400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:49395600-49406400	Weak transcription	Thymus	Thymus
21	chr6:49395800-49402400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:49395800-49406600	Weak transcription	Colonic Mucosa	Colon
23	chr6:49396000-49401000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:49396000-49401000	Weak transcription	Brain Anterior Caudate	brain
25	chr6:49396000-49402400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:49396000-49420800	Strong transcription	Liver	Liver
27	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:49396200-49420400	Strong transcription	Adipose Nuclei	Adipose
29	chr6:49396400-49403400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:49396400-49407600	Weak transcription	HSMMtube	muscle
31	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
32	chr6:49396600-49402000	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:49396600-49402400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:49396600-49408800	Strong transcription	Primary T cells from cord blood	blood
35	chr6:49396600-49411000	Weak transcription	Fetal Heart	heart
36	chr6:49396600-49412400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:49396800-49403200	Weak transcription	Pancreas	Pancrea
38	chr6:49396800-49404200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:49396800-49406200	Weak transcription	Aorta	Aorta
40	chr6:49396800-49406400	Weak transcription	Esophagus	oesophagus
41	chr6:49397000-49401000	Weak transcription	Placenta	Placenta
42	chr6:49397000-49413800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr6:49397000-49419800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr6:49397000-49425800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:49397200-49401200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:49397200-49402000	Weak transcription	Brain Substantia Nigra	brain
48	chr6:49397200-49402000	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:49397200-49404600	Strong transcription	Primary B cells from cord blood	blood
50	chr6:49397200-49421200	Strong transcription	Monocytes-CD14+_RO01746	blood

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