Variant report

Variant	rs11264339
Chromosome Location	chr1:155140648-155140649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:40)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:40 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155063588..155065472-chr1:155139784..155141178,19	K562	blood:
2	chr1:155050682..155052712-chr1:155140588..155142977,2	MCF-7	breast:
3	chr1:155138893..155143080-chr1:155146950..155151161,7	MCF-7	breast:
4	chr1:155066558..155067106-chr1:155140003..155140931,3	K562	blood:
5	chr1:155067274..155067813-chr1:155140046..155140799,2	K562	blood:
6	chr1:155034878..155035737-chr1:155140076..155140955,5	K562	blood:
7	chr1:155034065..155035215-chr1:155139817..155140992,3	MCF-7	breast:
8	chr1:155053391..155061594-chr1:155138130..155142281,13	MCF-7	breast:
9	chr1:155132887..155135800-chr1:155138561..155141355,2	K562	blood:
10	chr1:155052864..155055747-chr1:155138816..155141443,2	K562	blood:
11	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
12	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
13	chr1:155140499..155142005-chr1:155147734..155150654,2	K562	blood:
14	chr1:155065702..155067995-chr1:155139570..155140962,16	MCF-7	breast:
15	chr1:155056961..155061664-chr1:155139887..155142342,8	MCF-7	breast:
16	chr1:155057916..155058807-chr1:155140507..155141108,3	K562	blood:
17	chr1:155139584..155141986-chr1:155147016..155150073,3	MCF-7	breast:
18	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
19	chr1:155139118..155143025-chr1:155155964..155158470,4	MCF-7	breast:
20	chr1:155066076..155068136-chr1:155139564..155141486,24	MCF-7	breast:
21	chr1:155108466..155110343-chr1:155139689..155142610,2	K562	blood:
22	chr1:155058320..155058876-chr1:155140102..155140961,2	MCF-7	breast:
23	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
24	chr1:155140056..155140720-chr1:155149675..155150429,2	K562	blood:
25	chr1:155063589..155064900-chr1:155139461..155140960,10	MCF-7	breast:
26	chr1:155110780..155114663-chr1:155139164..155142857,6	MCF-7	breast:
27	chr1:155034862..155035730-chr1:155140353..155140934,2	MCF-7	breast:
28	chr1:155063515..155065067-chr1:155139525..155141192,27	MCF-7	breast:
29	chr1:155057235..155057812-chr1:155139947..155140960,4	K562	blood:
30	chr1:155096142..155099007-chr1:155138958..155141461,2	K562	blood:
31	chr1:155106324..155115462-chr1:155131611..155142074,22	MCF-7	breast:
32	chr1:155084815..155085826-chr1:155139557..155140946,6	MCF-7	breast:
33	chr1:155028322..155031856-chr1:155138984..155141470,4	MCF-7	breast:
34	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
35	chr1:155131988..155135383-chr1:155138366..155142220,5	MCF-7	breast:
36	chr1:155139047..155141231-chr1:155177826..155180456,2	K562	blood:
37	chr1:155034849..155038242-chr1:155138708..155141835,3	K562	blood:
38	chr1:155057083..155057726-chr1:155140410..155140940,2	MCF-7	breast:
39	chr1:155074516..155076079-chr1:155138849..155141341,2	MCF-7	breast:
40	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173171	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000163462	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10157801	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs10908458	1.00[CHB][hapmap]
rs11264337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799962	0.82[ASN][1000 genomes]
rs12025371	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12028043	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs12127609	0.82[ASN][1000 genomes]
rs12411216	0.85[ASN][1000 genomes]
rs12752585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs2066981	0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2075570	0.84[ASN][1000 genomes]
rs2075571	0.91[JPT][hapmap]
rs28445596	0.84[ASN][1000 genomes]
rs2974935	0.85[ASN][1000 genomes]
rs2974937	0.85[ASN][1000 genomes]
rs2990220	0.83[ASN][1000 genomes]
rs3814316	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4072037	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4246529	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4276913	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4276914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4421576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][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]
rs4460629	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4971052	0.90[CHB][hapmap]
rs4971059	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4971066	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4971073	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs4971076	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs4971079	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971085	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971088	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971093	0.82[ASN][1000 genomes]
rs4971100	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs6665822	0.80[GIH][hapmap]
rs6676150	0.93[AFR][1000 genomes]
rs7364524	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs7556304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760077	0.82[ASN][1000 genomes]
rs914615	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9297	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs9426886	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	407 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11264339	GBAP1	cis	Thyroid	GTEx
rs11264339	GBAP1	cis	lung	GTEx
rs11264339	THEM5	cis	parietal	SCAN
rs11264339	ADAM15	cis	multi-tissue	Pritchard
rs11264339	GBA	cis	lymphoblastoid	seeQTL
rs11264339	IVL	cis	parietal	SCAN
rs11264339	S100A7L2	cis	parietal	SCAN
rs11264339	RPRD2	cis	parietal	SCAN
rs11264339	THBS3	cis	Whole Blood	GTEx
rs11264339	GBA	cis	Esophagus Mucosa	GTEx
rs11264339	RP11-263K19.4	cis	Whole Blood	GTEx
rs11264339	GBAP1	cis	Artery Tibial	GTEx
rs11264339	PRUNE	cis	cerebellum	SCAN
rs11264339	SPRR4	cis	parietal	SCAN
rs11264339	CRNN	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155134200-155145000	Weak transcription	Small Intestine	intestine
2	chr1:155138400-155140800	Enhancers	Colonic Mucosa	Colon
3	chr1:155138800-155140800	Enhancers	Fetal Intestine Large	intestine
4	chr1:155139400-155140800	Enhancers	Liver	Liver
5	chr1:155139400-155140800	Enhancers	Dnd41	blood
6	chr1:155139600-155140800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:155139600-155140800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:155139600-155140800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:155139600-155140800	Enhancers	Fetal Heart	heart
10	chr1:155139600-155140800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:155139600-155140800	Enhancers	GM12878-XiMat	blood
12	chr1:155139600-155141200	Weak transcription	HSMMtube	muscle
13	chr1:155139800-155140800	Enhancers	Fetal Stomach	stomach
14	chr1:155139800-155140800	Enhancers	Fetal Thymus	thymus
15	chr1:155139800-155141400	Weak transcription	Aorta	Aorta
16	chr1:155140000-155140800	Enhancers	Stomach Mucosa	stomach
17	chr1:155140000-155141000	Weak transcription	Fetal Brain Female	brain
18	chr1:155140400-155140800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:155140400-155140800	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr1:155140400-155140800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr1:155140400-155141200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:155140400-155141200	Weak transcription	Esophagus	oesophagus
23	chr1:155140400-155141200	Weak transcription	Lung	lung
24	chr1:155140400-155141200	Weak transcription	HSMM	muscle
25	chr1:155140400-155141200	Weak transcription	Osteobl	bone
26	chr1:155140400-155141400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:155140400-155141400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:155140400-155141400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:155140400-155141400	Weak transcription	Primary T cells from cord blood	blood
30	chr1:155140400-155141400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:155140400-155141400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:155140400-155141400	Weak transcription	Left Ventricle	heart
33	chr1:155140400-155141400	Weak transcription	HMEC	breast
34	chr1:155140400-155141400	Weak transcription	NHDF-Ad	bronchial
35	chr1:155140400-155141600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:155140400-155141600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:155140400-155141600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:155140400-155141600	Weak transcription	Fetal Lung	lung
39	chr1:155140400-155141600	Weak transcription	Right Ventricle	heart
40	chr1:155140400-155141800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:155140400-155141800	Weak transcription	Fetal Brain Male	brain
42	chr1:155140400-155141800	Weak transcription	Pancreas	Pancrea
43	chr1:155140400-155141800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155140400-155142000	Weak transcription	Brain Substantia Nigra	brain
45	chr1:155140400-155144800	Weak transcription	Psoas Muscle	Psoas
46	chr1:155140600-155140800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:155140600-155140800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:155140600-155140800	Enhancers	Primary B cells from peripheral blood	blood
49	chr1:155140600-155140800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:155140600-155140800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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