Variant report

Variant	rs9473560
Chromosome Location	chr6:49427918-49427919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:49427784-49427947	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:49420777..49423406-chr6:49425809..49428236,2	K562	blood:
2	chr6:49352086..49353625-chr6:49427377..49430292,2	K562	blood:
3	chr6:49427543..49430477-chr6:49436132..49438156,2	K562	blood:

Variant related genes	Relation type
CENPQ	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10456622	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1141321	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196937	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12202075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209900	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212022	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086421	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147570	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448701	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2448702	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2448707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2477406	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493440	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501961	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501962	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501963	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501977	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501979	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501980	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3729619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823114	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957334	0.82[EUR][1000 genomes]
rs3997172	0.82[EUR][1000 genomes]
rs4267943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348317	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458686	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4469291	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4573082	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715129	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60944851	0.82[EUR][1000 genomes]
rs60982898	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411929	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411930	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411932	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458690	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458694	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901278	0.88[EUR][1000 genomes]
rs6909128	0.88[ASN][1000 genomes]
rs6923124	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7744595	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7750918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769018	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296616	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463473	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463474	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463475	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463476	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463477	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463479	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463480	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463483	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473547	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473549	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473551	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473552	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473553	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473555	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473557	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9473563	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473566	0.88[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9473560	CENPQ	cis	Thyroid	GTEx
rs9473560	MUT	cis	Nerve Tibial	GTEx
rs9473560	CENPQ	cis	Esophagus Muscularis	GTEx
rs9473560	CENPQ	cis	lung	GTEx
rs9473560	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9473560	CENPQ	cis	Artery Tibial	GTEx
rs9473560	CENPQ	cis	Nerve Tibial	GTEx
rs9473560	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9473560	MUT	cis	Artery Tibial	GTEx
rs9473560	MUT	cis	multi-tissue	Pritchard

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	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
3	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:49403400-49429600	Weak transcription	NHEK	skin
6	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
7	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
8	chr6:49407600-49428800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:49407800-49430400	Weak transcription	Lung	lung
13	chr6:49408000-49428200	Weak transcription	Fetal Brain Male	brain
14	chr6:49408000-49429200	Weak transcription	Thymus	Thymus
15	chr6:49408000-49430400	Weak transcription	Gastric	stomach
16	chr6:49408200-49428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
19	chr6:49408600-49429600	Weak transcription	K562	blood
20	chr6:49408800-49429200	Weak transcription	Small Intestine	intestine
21	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
23	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
27	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:49411200-49428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:49412000-49429200	Weak transcription	Psoas Muscle	Psoas
30	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:49412600-49429200	Weak transcription	Pancreas	Pancrea
32	chr6:49412600-49429400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:49412600-49429600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:49412600-49429600	Weak transcription	Fetal Heart	heart
35	chr6:49414400-49428200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:49416400-49429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:49416400-49429600	Weak transcription	HMEC	breast
38	chr6:49416600-49429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:49416800-49429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:49418800-49428800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:49418800-49429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:49419800-49430000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:49420800-49428000	Genic enhancers	Liver	Liver
44	chr6:49420800-49429600	Weak transcription	Osteobl	bone
45	chr6:49421600-49429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:49422600-49429400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:49422800-49428800	Weak transcription	Fetal Stomach	stomach
48	chr6:49422800-49429200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:49422800-49429400	Weak transcription	Fetal Intestine Small	intestine
50	chr6:49423200-49429200	Weak transcription	Spleen	Spleen

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