Variant report

Variant	rs7767725
Chromosome Location	chr6:49426018-49426019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49420777..49423406-chr6:49425809..49428236,2	K562	blood:
2	chr6:49423228..49426093-chr6:49579151..49581831,2	K562	blood:
3	chr6:49425386..49427485-chr6:49429135..49431175,2	MCF-7	breast:
4	chr6:49424647..49427636-chr6:49428636..49431243,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000031691	Chromatin interaction
ENSG00000146085	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12528625	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1471539	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2229384	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251115	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448704	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448705	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501959	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501960	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501964	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501965	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501966	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501968	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501978	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458685	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458688	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902429	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6915187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916888	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6918347	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6921413	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759071	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774688	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8589	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9349491	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369898	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9381784	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381787	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9381788	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9381789	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9395492	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395493	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463478	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9463482	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473550	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv603081	chr6:49421241-49446233	Weak transcription Active TSS Enhancers Flanking 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	10 gene(s)	inside rSNPs	diseases
5	nsv603082	chr6:49421241-49446509	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7767725	CENPQ	cis	Whole Blood	GTEx
rs7767725	CENPQ	cis	Esophagus Muscularis	GTEx
rs7767725	CENPQ	cis	Artery Tibial	GTEx
rs7767725	CENPQ	cis	multi-tissue	Pritchard
rs7767725	CENPQ	cis	lung	GTEx
rs7767725	CENPQ	cis	Artery Aorta	GTEx
rs7767725	CENPQ	cis	Adipose Subcutaneous	GTEx
rs7767725	MUT	cis	Artery Tibial	GTEx
rs7767725	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs7767725	CENPQ	cis	Nerve Tibial	GTEx
rs7767725	CENPQ	cis	Esophagus Mucosa	GTEx
rs7767725	CENPQ	cis	Muscle Skeletal	GTEx
rs7767725	MUT	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
4	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:49398400-49427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:49403400-49429600	Weak transcription	NHEK	skin
9	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
10	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
11	chr6:49407600-49428800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:49407800-49430400	Weak transcription	Lung	lung
16	chr6:49408000-49428200	Weak transcription	Fetal Brain Male	brain
17	chr6:49408000-49429200	Weak transcription	Thymus	Thymus
18	chr6:49408000-49430400	Weak transcription	Gastric	stomach
19	chr6:49408200-49428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
22	chr6:49408600-49429600	Weak transcription	K562	blood
23	chr6:49408800-49429200	Weak transcription	Small Intestine	intestine
24	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
26	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:49409000-49426200	Weak transcription	NHLF	lung
28	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
31	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:49411200-49428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:49412000-49429200	Weak transcription	Psoas Muscle	Psoas
34	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:49412600-49426400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:49412600-49429200	Weak transcription	Pancreas	Pancrea
37	chr6:49412600-49429400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:49412600-49429600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:49412600-49429600	Weak transcription	Fetal Heart	heart
40	chr6:49414400-49428200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:49416200-49427000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:49416400-49427600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:49416400-49429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:49416400-49429600	Weak transcription	HMEC	breast
45	chr6:49416600-49429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:49416800-49429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:49418600-49427000	Strong transcription	Fetal Lung	lung
48	chr6:49418800-49428800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:49418800-49429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:49419600-49426400	Weak transcription	NH-A	brain

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