Variant report

Variant	rs12637888
Chromosome Location	chr3:111527733-111527734
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	chr3:111521862..111524115-chr3:111526095..111528698,2	MCF-7	breast:
2	chr1:121484857..121485377-chr3:111526967..111527895,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10934110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717092	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4373041	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4472023	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4513422	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4610200	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682063	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438015	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs6438018	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772828	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772912	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772930	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6783431	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6794180	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6809414	0.86[JPT][hapmap]
rs7620045	0.86[EUR][1000 genomes]
rs9288930	0.82[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9814037	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816926	0.95[JPT][hapmap]
rs9817777	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9829968	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871340	0.87[EUR][1000 genomes]
rs9876709	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9880495	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12637888	PVRL3	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111514600-111533200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:111521200-111531000	Weak transcription	Small Intestine	intestine
3	chr3:111521800-111527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:111521800-111527800	Weak transcription	Stomach Mucosa	stomach
5	chr3:111522000-111528600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:111522400-111531400	Weak transcription	Fetal Lung	lung
7	chr3:111523000-111528200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:111523200-111527800	Weak transcription	NHLF	lung
9	chr3:111525800-111529000	Enhancers	Fetal Intestine Small	intestine
10	chr3:111526000-111531400	Enhancers	Hela-S3	cervix
11	chr3:111526200-111529000	Enhancers	Liver	Liver
12	chr3:111526400-111529000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:111526400-111529400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:111526400-111529400	Enhancers	Pancreas	Pancrea
15	chr3:111526400-111531000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:111526400-111531600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:111526400-111533000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:111526600-111528000	Flanking Active TSS	A549	lung
19	chr3:111526600-111531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:111526600-111532200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:111526600-111532200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:111526600-111532200	Enhancers	NHEK	skin
23	chr3:111526600-111533000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:111526600-111533000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:111526800-111528600	Enhancers	Colon Smooth Muscle	Colon
26	chr3:111526800-111529000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:111526800-111531400	Enhancers	HMEC	breast
28	chr3:111526800-111531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:111526800-111531800	Enhancers	Osteobl	bone
30	chr3:111526800-111532000	Enhancers	NHDF-Ad	bronchial
31	chr3:111526800-111532200	Enhancers	HSMM	muscle
32	chr3:111526800-111532600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:111527000-111529000	Enhancers	Fetal Kidney	kidney
34	chr3:111527000-111531200	Enhancers	NH-A	brain
35	chr3:111527000-111531600	Enhancers	HSMMtube	muscle
36	chr3:111527200-111528400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:111527200-111528600	Weak transcription	Aorta	Aorta
38	chr3:111527200-111529400	Enhancers	HepG2	liver
39	chr3:111527200-111530000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:111527400-111527800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:111527400-111527800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:111527400-111529200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:111527600-111528400	Weak transcription	Fetal Intestine Large	intestine

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