Variant report

Variant	rs1282970
Chromosome Location	chr3:111567238-111567239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111566221..111568973-chr3:111577173..111579400,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10212121	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10804493	0.86[EUR][1000 genomes]
rs10934112	1.00[JPT][hapmap]
rs10934114	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11711475	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs12490718	1.00[CEU][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs12695246	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs1282931	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1282932	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1282975	1.00[JPT][hapmap]
rs1282977	1.00[JPT][hapmap]
rs13063024	0.95[EUR][1000 genomes]
rs13063315	0.95[EUR][1000 genomes]
rs13083516	0.94[EUR][1000 genomes]
rs13101043	0.94[EUR][1000 genomes]
rs17490346	1.00[JPT][hapmap]
rs1913493	0.94[EUR][1000 genomes]
rs1913494	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs3925080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3925081	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4381907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4383483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4583615	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7626131	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7638138	0.89[EUR][1000 genomes]
rs937553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937554	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs967011	0.94[EUR][1000 genomes]
rs9814037	0.80[TSI][hapmap]
rs9827362	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9841149	1.00[JPT][hapmap]
rs9842341	1.00[JPT][hapmap]
rs9846313	0.94[EUR][1000 genomes]
rs9851613	0.93[JPT][hapmap]
rs9854765	1.00[JPT][hapmap]
rs9865074	1.00[JPT][hapmap]
rs9872438	1.00[JPT][hapmap]
rs9883806	0.96[CEU][hapmap];0.95[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
rs1282970	PVRL3	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111541200-111577600	Weak transcription	Pancreas	Pancrea
2	chr3:111559600-111567400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:111563000-111577400	Weak transcription	HepG2	liver
4	chr3:111563600-111568400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:111563800-111571200	Weak transcription	Stomach Mucosa	stomach
6	chr3:111564400-111567800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:111564400-111568400	Enhancers	NHEK	skin
8	chr3:111564600-111568000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:111564600-111568000	Enhancers	HMEC	breast
10	chr3:111564600-111568400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:111564600-111568400	Enhancers	Hela-S3	cervix
12	chr3:111564800-111567800	Strong transcription	Liver	Liver
13	chr3:111564800-111568200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:111564800-111568200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:111565000-111567600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:111565000-111571200	Enhancers	Placenta	Placenta
17	chr3:111565400-111569400	Weak transcription	NHLF	lung
18	chr3:111565600-111570200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:111565800-111570200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:111565800-111570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:111565800-111570600	Weak transcription	HSMM	muscle
22	chr3:111566000-111567400	Weak transcription	A549	lung
23	chr3:111566000-111569600	Weak transcription	Osteobl	bone
24	chr3:111566000-111571400	Weak transcription	Fetal Heart	heart
25	chr3:111566200-111567600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:111566200-111567600	Enhancers	HUVEC	blood vessel
27	chr3:111566200-111570000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:111566200-111570000	Weak transcription	NH-A	brain
29	chr3:111566200-111570400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:111566200-111577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:111566600-111567800	Enhancers	Small Intestine	intestine
32	chr3:111566800-111568000	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:111567200-111567600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:111567200-111567800	Enhancers	NHDF-Ad	bronchial
35	chr3:111567200-111568200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:111567200-111568400	Enhancers	Fetal Intestine Large	intestine
37	chr3:111567200-111570800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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