Variant report

Variant	rs4267639
Chromosome Location	chr3:50678151-50678152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1038415	0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs107457	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs11923336	1.00[EUR][1000 genomes]
rs13092850	1.00[EUR][1000 genomes]
rs1552255	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	1.00[EUR][1000 genomes]
rs17051016	1.00[EUR][1000 genomes]
rs17051017	1.00[EUR][1000 genomes]
rs17051404	1.00[EUR][1000 genomes]
rs1843073	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2129069	0.94[AFR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[EUR][1000 genomes]
rs2355337	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2355701	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2608994	0.82[AFR][1000 genomes]
rs2608996	0.82[AFR][1000 genomes]
rs2609004	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2609015	1.00[EUR][1000 genomes]
rs2609027	1.00[EUR][1000 genomes]
rs2609030	1.00[EUR][1000 genomes]
rs2675775	1.00[YRI][hapmap]
rs2675779	0.83[YRI][hapmap]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675798	0.81[AFR][1000 genomes]
rs2675815	0.83[YRI][hapmap]
rs2675823	1.00[EUR][1000 genomes]
rs2675824	1.00[EUR][1000 genomes]
rs2675826	1.00[EUR][1000 genomes]
rs2675833	0.82[ASW][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs407164	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs421689	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4234694	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4234695	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4340700	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4401355	1.00[EUR][1000 genomes]
rs4440121	1.00[EUR][1000 genomes]
rs4688675	1.00[EUR][1000 genomes]
rs4688704	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4688717	1.00[EUR][1000 genomes]
rs55852678	1.00[EUR][1000 genomes]
rs56112107	1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56413944	1.00[EUR][1000 genomes]
rs57756789	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57987466	1.00[EUR][1000 genomes]
rs58854038	1.00[EUR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59065723	1.00[EUR][1000 genomes]
rs59337835	1.00[EUR][1000 genomes]
rs59340349	1.00[EUR][1000 genomes]
rs59944295	1.00[EUR][1000 genomes]
rs60132317	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60455882	1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	1.00[EUR][1000 genomes]
rs61455710	1.00[EUR][1000 genomes]
rs621975	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs628865	0.82[ASW][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446223	1.00[EUR][1000 genomes]
rs650473	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	1.00[EUR][1000 genomes]
rs6789552	1.00[EUR][1000 genomes]
rs73833231	1.00[EUR][1000 genomes]
rs73833232	1.00[EUR][1000 genomes]
rs73833239	1.00[EUR][1000 genomes]
rs73833247	1.00[EUR][1000 genomes]
rs73833935	1.00[EUR][1000 genomes]
rs73833947	1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	1.00[EUR][1000 genomes]
rs73835535	1.00[EUR][1000 genomes]
rs73835537	1.00[EUR][1000 genomes]
rs73835538	1.00[EUR][1000 genomes]
rs7650772	1.00[EUR][1000 genomes]
rs7653228	1.00[EUR][1000 genomes]
rs936714	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9825283	0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9840476	0.82[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9851304	1.00[EUR][1000 genomes]
rs9857033	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4267639	PRPF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
2	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
4	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:50665400-50679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
9	chr3:50667200-50680400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:50668600-50678800	Weak transcription	Pancreas	Pancrea
11	chr3:50668600-50679200	Weak transcription	HepG2	liver
12	chr3:50669000-50684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:50670200-50689000	Weak transcription	K562	blood
14	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
15	chr3:50670800-50679800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:50671200-50679000	Weak transcription	Ovary	ovary
17	chr3:50671200-50680600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:50672400-50680600	Weak transcription	GM12878-XiMat	blood
19	chr3:50672400-50688000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:50674000-50681400	Weak transcription	Fetal Kidney	kidney
21	chr3:50674200-50679200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:50674200-50687200	Strong transcription	Dnd41	blood
23	chr3:50674400-50681800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:50674600-50678600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:50674800-50678400	Weak transcription	Fetal Lung	lung
26	chr3:50674800-50679600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:50674800-50680800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:50675400-50682400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:50675400-50687400	Strong transcription	Thymus	Thymus
30	chr3:50675600-50678400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:50675600-50681600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:50675600-50684600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:50675800-50679200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:50675800-50688000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:50676000-50686000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:50676000-50687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:50676000-50688200	Strong transcription	Primary T cells from cord blood	blood
38	chr3:50676000-50689200	Strong transcription	Fetal Intestine Small	intestine
39	chr3:50676200-50679000	Weak transcription	Brain Anterior Caudate	brain
40	chr3:50676200-50679600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:50676200-50686600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:50676200-50686600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:50676200-50686800	Strong transcription	Lung	lung
44	chr3:50676400-50678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:50676400-50678200	Weak transcription	Psoas Muscle	Psoas
46	chr3:50676400-50678800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:50676400-50681200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:50676400-50682600	Strong transcription	Spleen	Spleen
49	chr3:50676400-50686000	Strong transcription	Fetal Stomach	stomach
50	chr3:50676400-50686800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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