Variant report

Variant	rs4276914
Chromosome Location	chr1:155142229-155142230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155142111-155142423	K562	blood:	n/a	n/a
2	POLR2A	chr1:155141920-155142663	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr1:155142023-155142499	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:155140371-155142652	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:155142134-155142489	K562	blood:	n/a	n/a
6	POLR2A	chr1:155140963-155142512	SK-N-MC	brain:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155050682..155052712-chr1:155140588..155142977,2	MCF-7	breast:
2	chr1:155138893..155143080-chr1:155146950..155151161,7	MCF-7	breast:
3	chr1:155053391..155061594-chr1:155138130..155142281,13	MCF-7	breast:
4	chr1:155027331..155029018-chr1:155140690..155142763,2	K562	blood:
5	chr1:155041712..155043919-chr1:155142054..155144015,2	K562	blood:
6	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
7	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
8	chr1:155056961..155061664-chr1:155139887..155142342,8	MCF-7	breast:
9	chr1:155019549..155021097-chr1:155141085..155143044,2	MCF-7	breast:
10	chr1:155066673..155067248-chr1:155141597..155142397,2	MCF-7	breast:
11	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
12	chr1:155139118..155143025-chr1:155155964..155158470,4	MCF-7	breast:
13	chr1:155108466..155110343-chr1:155139689..155142610,2	K562	blood:
14	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
15	chr1:155110780..155114663-chr1:155139164..155142857,6	MCF-7	breast:
16	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
17	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM46	TF binding region
ENSG00000169242	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000163462	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157801	0.82[ASN][1000 genomes]
rs11264337	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799962	0.82[ASN][1000 genomes]
rs12028043	0.82[ASN][1000 genomes]
rs12127609	0.82[ASN][1000 genomes]
rs12411216	0.85[ASN][1000 genomes]
rs12752585	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075570	0.84[ASN][1000 genomes]
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	0.81[ASN][1000 genomes]
rs4276913	0.82[ASN][1000 genomes]
rs4421576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460629	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971059	0.81[ASN][1000 genomes]
rs4971076	0.82[ASN][1000 genomes]
rs4971079	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971093	0.82[ASN][1000 genomes]
rs6676150	0.91[AFR][1000 genomes]
rs7364524	0.82[ASN][1000 genomes]
rs7556304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760077	0.82[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4276914	GBAP1	cis	lung	GTEx
rs4276914	GBA	cis	Esophagus Mucosa	GTEx
rs4276914	THBS3	cis	Whole Blood	GTEx
rs4276914	GBAP1	cis	Artery Tibial	GTEx
rs4276914	RP11-263K19.4	cis	Whole Blood	GTEx
rs4276914	GBAP1	cis	Thyroid	GTEx

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	chr1:155140400-155144800	Weak transcription	Psoas Muscle	Psoas
3	chr1:155140600-155144000	Weak transcription	Hela-S3	cervix
4	chr1:155140600-155144600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:155140600-155144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:155140600-155144600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:155140800-155144000	Weak transcription	HepG2	liver
8	chr1:155140800-155144200	Weak transcription	GM12878-XiMat	blood
9	chr1:155140800-155144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:155140800-155144600	Weak transcription	Stomach Mucosa	stomach
11	chr1:155141000-155143200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:155141000-155143200	Strong transcription	Fetal Kidney	kidney
13	chr1:155141000-155143400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:155141000-155143400	Strong transcription	Fetal Brain Female	brain
15	chr1:155141000-155143600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:155141000-155143800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:155141000-155144000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:155141000-155144200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:155141000-155144200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:155141000-155144200	Strong transcription	Spleen	Spleen
21	chr1:155141000-155144600	Strong transcription	Fetal Intestine Small	intestine
22	chr1:155141200-155142600	Strong transcription	Esophagus	oesophagus
23	chr1:155141200-155142600	Strong transcription	HSMMtube	muscle
24	chr1:155141200-155143000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:155141200-155143000	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:155141200-155143200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:155141200-155143200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:155141200-155143200	Strong transcription	Brain Angular Gyrus	brain
29	chr1:155141200-155143200	Strong transcription	Brain Anterior Caudate	brain
30	chr1:155141200-155143200	Strong transcription	Brain Hippocampus Middle	brain
31	chr1:155141200-155143200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:155141200-155143200	Strong transcription	Rectal Smooth Muscle	rectum
33	chr1:155141200-155143200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:155141200-155143200	Strong transcription	Thymus	Thymus
35	chr1:155141200-155143200	Strong transcription	A549	lung
36	chr1:155141200-155143200	Strong transcription	Osteobl	bone
37	chr1:155141200-155143400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:155141200-155143400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:155141200-155143400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:155141200-155143600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:155141200-155143600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:155141200-155143600	Strong transcription	HSMM	muscle
43	chr1:155141200-155143800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:155141200-155144000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:155141200-155144000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:155141200-155144000	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:155141200-155144000	Strong transcription	Fetal Stomach	stomach
48	chr1:155141200-155144000	Strong transcription	Dnd41	blood
49	chr1:155141200-155144200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:155141200-155144200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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