Variant report

Variant	rs4715131
Chromosome Location	chr6:49429264-49429265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49428636..49430625-chr6:49435581..49438306,2	MCF-7	breast:
2	chr6:49352086..49353625-chr6:49427377..49430292,2	K562	blood:
3	chr6:49419838..49421598-chr6:49428414..49430900,2	K562	blood:
4	chr6:49428075..49430840-chr6:49629508..49632761,3	K562	blood:
5	chr6:49428409..49430841-chr6:49452599..49454961,2	K562	blood:
6	chr6:49427543..49430477-chr6:49436132..49438156,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10456622	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1141321	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196937	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12202075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209900	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212022	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086421	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147570	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448701	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2448702	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2448707	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477405	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2477406	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493440	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501961	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501962	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501963	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501979	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501980	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3729619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823114	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957334	0.80[EUR][1000 genomes]
rs3997172	0.80[EUR][1000 genomes]
rs4267943	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348317	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458686	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4469291	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4573082	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715129	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715130	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60944851	0.80[EUR][1000 genomes]
rs60982898	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411929	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411930	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411932	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458690	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458694	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901278	0.86[EUR][1000 genomes]
rs6909128	0.88[ASN][1000 genomes]
rs6923124	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7744595	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7750918	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769018	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296616	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463473	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463474	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463475	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463476	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463477	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463479	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463480	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463483	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473547	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473549	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473552	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473553	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473555	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473557	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9473563	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473566	0.86[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4715131	CENPQ	cis	Esophagus Muscularis	GTEx
rs4715131	CENPQ	cis	Artery Tibial	GTEx
rs4715131	CENPQ	cis	Nerve Tibial	GTEx
rs4715131	MUT	cis	Nerve Tibial	GTEx
rs4715131	CENPQ	cis	Thyroid	GTEx
rs4715131	CENPQ	cis	Adipose Subcutaneous	GTEx
rs4715131	CENPQ	cis	lung	GTEx
rs4715131	MUT	cis	Artery Tibial	GTEx
rs4715131	MUT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr6:49403400-49429600	Weak transcription	NHEK	skin
5	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
6	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
7	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:49407800-49430400	Weak transcription	Lung	lung
11	chr6:49408000-49430400	Weak transcription	Gastric	stomach
12	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
14	chr6:49408600-49429600	Weak transcription	K562	blood
15	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
17	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
21	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:49412600-49429400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:49412600-49429600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:49412600-49429600	Weak transcription	Fetal Heart	heart
26	chr6:49416400-49429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:49416400-49429600	Weak transcription	HMEC	breast
28	chr6:49416600-49429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:49416800-49429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:49418800-49429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:49419800-49430000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:49420800-49429600	Weak transcription	Osteobl	bone
33	chr6:49421600-49429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:49422600-49429400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:49422800-49429400	Weak transcription	Fetal Intestine Small	intestine
36	chr6:49423200-49429800	Weak transcription	Aorta	Aorta
37	chr6:49423400-49429400	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:49423400-49429800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:49423400-49429800	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:49424800-49429600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:49425000-49429400	Weak transcription	Primary T cells from cord blood	blood
42	chr6:49425000-49429600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:49425000-49429800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:49425600-49429400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:49425600-49429600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:49425800-49429600	Weak transcription	Brain Anterior Caudate	brain
47	chr6:49425800-49429600	Weak transcription	Fetal Intestine Large	intestine
48	chr6:49425800-49429800	Weak transcription	Left Ventricle	heart
49	chr6:49426000-49429600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:49426000-49429800	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links