Variant report

Variant	rs1472253
Chromosome Location	chr1:220882826-220882827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12032280	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12407624	1.00[ASW][hapmap];0.89[CEU][hapmap]
rs12410279	0.87[AMR][1000 genomes]
rs12563921	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12564479	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs337163	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337166	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337167	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337168	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337174	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337182	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs337188	0.82[EUR][1000 genomes]
rs337192	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3806329	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs382451	0.85[EUR][1000 genomes]
rs4846658	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59423796	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61830219	0.90[AMR][1000 genomes]
rs61830238	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6689349	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72629673	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs774139	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs796486	0.82[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	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1472253	C1orf115	cis	cerebellum	SCAN
rs1472253	TGFB2	cis	cerebellum	SCAN
rs1472253	C1orf115	cis	multi-tissue	Pritchard
rs1472253	MOSC1	cis	parietal	SCAN
rs1472253	EPRS	cis	cerebellum	SCAN
rs1472253	MOSC2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220878200-220883800	Enhancers	Fetal Intestine Small	intestine
2	chr1:220878400-220885200	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:220878400-220886000	Enhancers	HepG2	liver
4	chr1:220878800-220885200	Enhancers	Pancreas	Pancrea
5	chr1:220879400-220884400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:220879600-220883400	Weak transcription	Adipose Nuclei	Adipose
7	chr1:220880400-220883000	Weak transcription	Gastric	stomach
8	chr1:220880400-220883600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:220880800-220883400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:220881200-220883000	Weak transcription	Ovary	ovary
11	chr1:220881600-220883400	Enhancers	Fetal Intestine Large	intestine
12	chr1:220881600-220885200	Enhancers	Primary B cells from cord blood	blood
13	chr1:220881600-220885200	Enhancers	Liver	Liver
14	chr1:220881600-220885400	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:220881800-220883200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:220882000-220883400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:220882000-220884400	Weak transcription	Small Intestine	intestine
18	chr1:220882400-220885000	Enhancers	Right Ventricle	heart
19	chr1:220882600-220883200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:220882600-220883200	Enhancers	Stomach Mucosa	stomach
21	chr1:220882600-220884800	Enhancers	Right Atrium	heart
22	chr1:220882600-220884800	Enhancers	Spleen	Spleen
23	chr1:220882800-220884000	Enhancers	Lung	lung
24	chr1:220882800-220884600	Weak transcription	Fetal Lung	lung
25	chr1:220882800-220885200	Enhancers	Left Ventricle	heart

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