Variant report

Variant	rs4953589
Chromosome Location	chr2:48740195-48740196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48739322..48741224-chr2:48741836..48744392,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12472635	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12615167	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3811522	0.84[JPT][hapmap]
rs4434042	0.84[JPT][hapmap]
rs4443044	0.91[LWK][hapmap];0.92[YRI][hapmap]
rs4497915	0.91[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap]
rs4597580	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606562	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4953589	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4953589	CRIPT	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
2	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
5	chr2:48722600-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
7	chr2:48726200-48742400	Weak transcription	Colonic Mucosa	Colon
8	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:48728200-48756800	Weak transcription	HMEC	breast
10	chr2:48728800-48741800	Weak transcription	Spleen	Spleen
11	chr2:48729000-48742800	Weak transcription	Right Ventricle	heart
12	chr2:48729600-48742800	Weak transcription	Esophagus	oesophagus
13	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:48732400-48743400	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
16	chr2:48733400-48742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:48735400-48740200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:48735400-48740400	Strong transcription	Brain Germinal Matrix	brain
19	chr2:48735600-48740200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:48736000-48741800	Weak transcription	Fetal Brain Female	brain
21	chr2:48736000-48742800	Weak transcription	Aorta	Aorta
22	chr2:48736000-48742800	Weak transcription	Gastric	stomach
23	chr2:48736000-48742800	Weak transcription	Ovary	ovary
24	chr2:48736000-48742800	Weak transcription	Pancreas	Pancrea
25	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
26	chr2:48736200-48749400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:48736200-48749400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:48736400-48742600	Weak transcription	Stomach Mucosa	stomach
29	chr2:48736400-48748400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:48736400-48749600	Strong transcription	Liver	Liver
31	chr2:48736400-48750000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:48736400-48752600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:48736400-48753400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:48736400-48754600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:48736600-48746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:48736600-48749600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:48736600-48749800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:48736800-48747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:48736800-48749400	Strong transcription	Fetal Thymus	thymus
40	chr2:48736800-48749600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:48737000-48744400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:48737000-48748200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:48737000-48748600	Strong transcription	Dnd41	blood
44	chr2:48737000-48749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:48737000-48749600	Strong transcription	Brain Anterior Caudate	brain
46	chr2:48737200-48750600	Strong transcription	Fetal Intestine Large	intestine
47	chr2:48737400-48747000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:48737600-48744800	Strong transcription	HepG2	liver
49	chr2:48737600-48747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:48737600-48749800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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