Variant report

Variant	rs9381784
Chromosome Location	chr6:49398115-49398116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49395795..49399005-chr6:49401983..49404851,4	K562	blood:
2	chr6:49375571..49377870-chr6:49396381..49398222,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12528625	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471539	0.83[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2229384	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251115	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2448704	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2448705	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2493441	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501959	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2501960	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501964	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501965	0.83[EUR][1000 genomes]
rs2501966	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2501968	0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2501978	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502946	1.00[ASW][hapmap]
rs562077	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs6458685	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458688	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902429	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915187	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916888	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6918347	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921413	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7759071	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767725	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7774688	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8589	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349491	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369898	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381785	0.80[ASN][1000 genomes]
rs9381787	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381788	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381789	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395492	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9395493	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463478	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9463482	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473550	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9381784	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs9381784	CENPQ	cis	lymphoblastoid	seeQTL
rs9381784	CENPQ	cis	lung	GTEx
rs9381784	CENPQ	cis	Muscle Skeletal	GTEx
rs9381784	CENPQ	cis	Esophagus Mucosa	GTEx
rs9381784	CENPQ	cis	multi-tissue	Pritchard
rs9381784	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9381784	CENPQ	cis	Artery Tibial	GTEx
rs9381784	C6orf139	cis	normal skin	skin_eQTL
rs9381784	CENPQ	cis	Nerve Tibial	GTEx
rs9381784	MUT	cis	Nerve Tibial	GTEx
rs9381784	CENPQ	cis	Esophagus Muscularis	GTEx
rs9381784	MUT	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49383400-49399800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:49384200-49398400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:49389600-49401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:49391000-49401200	Weak transcription	Left Ventricle	heart
5	chr6:49392400-49398800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:49392400-49403800	Weak transcription	Right Ventricle	heart
7	chr6:49392800-49400400	Weak transcription	Ovary	ovary
8	chr6:49393400-49406400	Weak transcription	Lung	lung
9	chr6:49393600-49399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:49394000-49400400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:49394600-49398800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:49394600-49399200	Weak transcription	Brain Germinal Matrix	brain
13	chr6:49394600-49399600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:49394600-49400200	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:49394800-49398800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:49394800-49403200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:49395000-49402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:49395200-49398600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:49395200-49399200	Weak transcription	Fetal Lung	lung
20	chr6:49395200-49400400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:49395200-49400400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:49395200-49406400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:49395200-49406400	Weak transcription	Fetal Stomach	stomach
24	chr6:49395200-49406400	Weak transcription	Gastric	stomach
25	chr6:49395200-49406400	Weak transcription	Spleen	Spleen
26	chr6:49395400-49400800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:49395400-49400800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:49395400-49400800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:49395400-49402400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:49395400-49406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:49395600-49400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:49395600-49403200	Weak transcription	Psoas Muscle	Psoas
34	chr6:49395600-49406400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:49395600-49406400	Weak transcription	Thymus	Thymus
36	chr6:49395800-49398400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:49395800-49399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:49395800-49400400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:49395800-49400400	Weak transcription	Fetal Kidney	kidney
40	chr6:49395800-49402400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:49395800-49406600	Weak transcription	Colonic Mucosa	Colon
42	chr6:49396000-49401000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:49396000-49401000	Weak transcription	Brain Anterior Caudate	brain
44	chr6:49396000-49402400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:49396000-49420800	Strong transcription	Liver	Liver
46	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:49396200-49420400	Strong transcription	Adipose Nuclei	Adipose
48	chr6:49396400-49398400	Strong transcription	Fetal Brain Female	brain
49	chr6:49396400-49403400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:49396400-49407600	Weak transcription	HSMMtube	muscle

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