Variant report

Variant	rs4952915
Chromosome Location	chr2:48749800-48749801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12615167	0.96[ASN][1000 genomes]
rs12618125	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4293602	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296472	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4528813	0.85[ASN][1000 genomes]
rs4597580	0.86[ASN][1000 genomes]
rs4641991	0.84[ASN][1000 genomes]
rs4952914	0.96[ASN][1000 genomes]
rs4953587	0.88[ASN][1000 genomes]
rs6545046	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545047	0.97[ASN][1000 genomes]
rs6754946	0.96[ASN][1000 genomes]
rs7569575	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs4952915	GTF2A1L	cis	Esophagus Muscularis	GTEx
rs4952915	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:125 , 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	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:48728200-48756800	Weak transcription	HMEC	breast
5	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
7	chr2:48736400-48750000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:48736400-48752600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:48736400-48753400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:48736400-48754600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:48736600-48749800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:48737200-48750600	Strong transcription	Fetal Intestine Large	intestine
13	chr2:48737600-48749800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:48737600-48750200	Strong transcription	Primary T cells from cord blood	blood
15	chr2:48737800-48750000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:48737800-48752000	Strong transcription	Fetal Intestine Small	intestine
17	chr2:48737800-48756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:48738000-48750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:48738000-48755400	Weak transcription	HUVEC	blood vessel
20	chr2:48738000-48756800	Weak transcription	NH-A	brain
21	chr2:48738200-48753800	Weak transcription	Hela-S3	cervix
22	chr2:48740000-48754400	Weak transcription	NHLF	lung
23	chr2:48740000-48756000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:48740000-48757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:48741000-48753000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:48742400-48756200	Weak transcription	NHDF-Ad	bronchial
27	chr2:48743000-48754600	Weak transcription	Fetal Kidney	kidney
28	chr2:48743200-48756000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:48743200-48756200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:48743200-48756800	Weak transcription	Stomach Mucosa	stomach
31	chr2:48743400-48749800	Strong transcription	Fetal Stomach	stomach
32	chr2:48743400-48753000	Weak transcription	Fetal Heart	heart
33	chr2:48743400-48753000	Weak transcription	Right Ventricle	heart
34	chr2:48743400-48756200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:48743400-48756400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:48743400-48757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:48743400-48757400	Weak transcription	Gastric	stomach
38	chr2:48743800-48752800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:48744000-48752400	Weak transcription	K562	blood
40	chr2:48744000-48756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:48744000-48756800	Weak transcription	Colonic Mucosa	Colon
42	chr2:48744600-48752800	Weak transcription	Pancreas	Pancrea
43	chr2:48744600-48753200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:48744600-48754800	Weak transcription	HSMMtube	muscle
45	chr2:48744600-48756400	Weak transcription	Brain Germinal Matrix	brain
46	chr2:48744800-48755800	Weak transcription	HepG2	liver
47	chr2:48744800-48756200	Weak transcription	Fetal Brain Female	brain
48	chr2:48745200-48756200	Weak transcription	Esophagus	oesophagus
49	chr2:48745600-48752800	Weak transcription	Left Ventricle	heart
50	chr2:48745600-48753000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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