Variant report

Variant	rs6458688
Chromosome Location	chr6:49406056-49406057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:47794827..47796539-chr6:49405343..49408041,2	K562	blood:
2	chr6:49404012..49406984-chr6:49407008..49409113,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12528625	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1471539	0.88[EUR][1000 genomes]
rs2229384	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251115	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2448704	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2448705	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2493441	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2501959	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2501960	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501964	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501965	0.88[EUR][1000 genomes]
rs2501966	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2501968	0.88[EUR][1000 genomes]
rs2501978	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458685	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6902429	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915187	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916888	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6918347	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921413	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7759071	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767725	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7774688	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8589	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349491	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9369898	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9381784	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381785	0.81[ASN][1000 genomes]
rs9381787	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381788	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381789	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395492	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9395493	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463478	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463482	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473550	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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
rs6458688	MUT	cis	Nerve Tibial	GTEx
rs6458688	CENPQ	cis	Adipose Subcutaneous	GTEx
rs6458688	CENPQ	cis	Esophagus Mucosa	GTEx
rs6458688	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs6458688	CENPQ	cis	Artery Aorta	GTEx
rs6458688	CENPQ	cis	lung	GTEx
rs6458688	CENPQ	cis	Muscle Skeletal	GTEx
rs6458688	CENPQ	cis	multi-tissue	Pritchard
rs6458688	CENPQ	cis	Whole Blood	GTEx
rs6458688	CENPQ	cis	Nerve Tibial	GTEx
rs6458688	CENPQ	cis	Artery Tibial	GTEx
rs6458688	MUT	cis	Artery Tibial	GTEx
rs6458688	CENPQ	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49393400-49406400	Weak transcription	Lung	lung
2	chr6:49395200-49406400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:49395200-49406400	Weak transcription	Fetal Stomach	stomach
4	chr6:49395200-49406400	Weak transcription	Gastric	stomach
5	chr6:49395200-49406400	Weak transcription	Spleen	Spleen
6	chr6:49395400-49406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:49395600-49406400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:49395600-49406400	Weak transcription	Thymus	Thymus
10	chr6:49395800-49406600	Weak transcription	Colonic Mucosa	Colon
11	chr6:49396000-49420800	Strong transcription	Liver	Liver
12	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:49396200-49420400	Strong transcription	Adipose Nuclei	Adipose
14	chr6:49396400-49407600	Weak transcription	HSMMtube	muscle
15	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
16	chr6:49396600-49408800	Strong transcription	Primary T cells from cord blood	blood
17	chr6:49396600-49411000	Weak transcription	Fetal Heart	heart
18	chr6:49396600-49412400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:49396800-49406200	Weak transcription	Aorta	Aorta
20	chr6:49396800-49406400	Weak transcription	Esophagus	oesophagus
21	chr6:49397000-49413800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:49397000-49419800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:49397000-49425800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:49397200-49421200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:49397400-49412600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:49397400-49425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:49397400-49426000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:49397800-49419800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:49397800-49420000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:49398000-49412600	Strong transcription	Fetal Intestine Large	intestine
32	chr6:49398200-49407800	Weak transcription	Small Intestine	intestine
33	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:49398400-49425600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:49398400-49427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:49398600-49420000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:49398800-49408800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:49398800-49412600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:49398800-49413200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:49398800-49418800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:49399000-49407200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:49399000-49408200	Weak transcription	K562	blood
43	chr6:49399000-49412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:49399200-49412600	Strong transcription	Fetal Thymus	thymus
45	chr6:49399400-49408600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:49399600-49407800	Weak transcription	Hela-S3	cervix
47	chr6:49399600-49408800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:49399800-49406400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:49399800-49412400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr6:49399800-49420800	Weak transcription	H1 Cell Line	embryonic stem cell

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