Variant report

Variant	rs9872438
Chromosome Location	chr3:111543285-111543286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10934112	1.00[JPT][hapmap]
rs10934114	1.00[JPT][hapmap]
rs1282970	1.00[JPT][hapmap]
rs1282975	1.00[JPT][hapmap]
rs1282977	1.00[JPT][hapmap]
rs17490346	1.00[JPT][hapmap]
rs3925080	1.00[JPT][hapmap]
rs3925081	1.00[JPT][hapmap]
rs4381907	1.00[JPT][hapmap]
rs4383483	1.00[JPT][hapmap]
rs55842003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73226309	0.88[EUR][1000 genomes]
rs73226316	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73226326	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73226334	1.00[ASN][1000 genomes]
rs7637689	1.00[JPT][hapmap]
rs937553	1.00[JPT][hapmap]
rs937554	1.00[JPT][hapmap]
rs9836042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841149	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9842341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854765	1.00[JPT][hapmap]
rs9865074	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs9872438	PVRL3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111539600-111545400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:111541000-111544200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:111541000-111550600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:111541200-111577600	Weak transcription	Pancreas	Pancrea
5	chr3:111541400-111543400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:111541800-111543600	Enhancers	Right Ventricle	heart
7	chr3:111542000-111543800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:111542000-111545600	Weak transcription	Lung	lung
9	chr3:111542400-111543600	Enhancers	Left Ventricle	heart
10	chr3:111542600-111543600	Enhancers	Fetal Heart	heart
11	chr3:111542800-111543400	Enhancers	Placenta	Placenta
12	chr3:111542800-111543600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:111542800-111544400	Strong transcription	Liver	Liver
14	chr3:111543000-111543600	Enhancers	Adipose Nuclei	Adipose
15	chr3:111543200-111543600	Enhancers	Ovary	ovary
16	chr3:111543200-111543600	Enhancers	Right Atrium	heart

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