Variant report

Variant	rs9473553
Chromosome Location	chr6:49395977-49395978
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	chr6:49393144..49396120-chr6:49398943..49401576,2	K562	blood:
2	chr6:49395795..49399005-chr6:49401983..49404851,4	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141321	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196937	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202075	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209900	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212022	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086421	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147570	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448701	0.83[EUR][1000 genomes]
rs2448702	0.83[EUR][1000 genomes]
rs2448707	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477405	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477406	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493440	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501961	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501962	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501963	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501977	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501979	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501980	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729619	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806988	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823114	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267943	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4348317	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458686	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469291	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4573082	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715129	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715130	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715131	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60982898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411929	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411930	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411932	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458690	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458693	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458694	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901278	0.82[EUR][1000 genomes]
rs6909128	0.92[ASN][1000 genomes]
rs6923124	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744595	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750918	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769018	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296616	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296617	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463474	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463476	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463479	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463480	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463483	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473547	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473549	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473551	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473552	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473555	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473557	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473560	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473561	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473563	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473566	0.82[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
rs9473553	MUT	cis	Artery Tibial	GTEx
rs9473553	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9473553	CENPQ	cis	Esophagus Muscularis	GTEx
rs9473553	MUT	cis	Nerve Tibial	GTEx
rs9473553	CENPQ	cis	lung	GTEx
rs9473553	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9473553	MUT	cis	multi-tissue	Pritchard
rs9473553	CENPQ	cis	Thyroid	GTEx
rs9473553	CENPQ	cis	Nerve Tibial	GTEx
rs9473553	CENPQ	cis	Artery Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49382000-49396600	Weak transcription	Aorta	Aorta
2	chr6:49383400-49399800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:49384200-49398400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:49389600-49401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:49391000-49401200	Weak transcription	Left Ventricle	heart
6	chr6:49392400-49396000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:49392400-49398800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:49392400-49403800	Weak transcription	Right Ventricle	heart
9	chr6:49392600-49396600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:49392600-49397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:49392800-49400400	Weak transcription	Ovary	ovary
12	chr6:49393400-49406400	Weak transcription	Lung	lung
13	chr6:49393600-49399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:49394000-49400400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:49394400-49396000	Weak transcription	Liver	Liver
16	chr6:49394600-49396200	Weak transcription	Adipose Nuclei	Adipose
17	chr6:49394600-49397000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:49394600-49398800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:49394600-49399200	Weak transcription	Brain Germinal Matrix	brain
20	chr6:49394600-49399600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:49394600-49400200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:49394800-49396400	Weak transcription	Fetal Brain Female	brain
23	chr6:49394800-49396400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:49394800-49397200	Weak transcription	Primary B cells from cord blood	blood
25	chr6:49394800-49397400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:49394800-49398800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:49394800-49403200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:49395000-49396600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:49395000-49402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:49395200-49396800	Weak transcription	Fetal Thymus	thymus
31	chr6:49395200-49398600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:49395200-49399200	Weak transcription	Fetal Lung	lung
33	chr6:49395200-49400400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:49395200-49400400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:49395200-49406400	Weak transcription	Fetal Intestine Small	intestine
36	chr6:49395200-49406400	Weak transcription	Fetal Stomach	stomach
37	chr6:49395200-49406400	Weak transcription	Gastric	stomach
38	chr6:49395200-49406400	Weak transcription	Spleen	Spleen
39	chr6:49395400-49397000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:49395400-49397000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:49395400-49397000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:49395400-49400800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:49395400-49400800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr6:49395400-49400800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:49395400-49402400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:49395400-49406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:49395600-49397200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:49395600-49400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:49395600-49403200	Weak transcription	Psoas Muscle	Psoas

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