Reference SNP(refSNP) Cluster Report: rs12720579

Reference SNP(refSNP) Cluster Report: rs12720579

refSNP ID: rs12720579
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_024420.2:c.559-5052G>A
NT_004487.18:g.37387197G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss20418471 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12720579 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss20418471	EGP_SNPS\|PLA2G4A-100241		fwd/T	A/G	aaaatatggaccttaagtaattaattctcc	agtgccacttggtacttgtcatataagtta	02/25/04	03/04/04	121	Genomic			unknown

Fasta sequence (Legend)

 AAATGAAATG TTACTATCCA GTCTCTATGT CCCCTAAAAA CTAGCCATAC CATAACGCGG
 TTGGTTGGGG GAGTAAAATC TGGAATTAGA GTAGTAAAGA AATGAGAGAA GAAAAGATTC
 TTCTTGTCAT CAGAGTGTAA AAGAGATAAT GCTTTTTCTT AAGGAAGACA ATAAGGACCA
 TATTTCAGTT TAAACAAATA GACAGCTTTG GATGAAAATA GAAGTAAAAT ATGGACCTTA
 AGTAATTAAT TCTCC
 R
 AGTGCCACTT GGTACTTGTC ATATAAGTTA AGTGAAAGTC TAGAGAAAGA CAGATCATCT
 AGTCATGGAG GGAGAGGCAG AGCAAGACAG TTTCTTCTGA AGGAGATAAG AGAAATCAAC
 CTTGAGTTGT CAATAAGCAT TTCCATTCCT ATGTTTCTGT TGTTTCCTTC ATCGAGAATA
 TTTCCTCGCC TCTTTCCACC TTCATTCTGA CAATGGCACT TTGTGCTATC AATCTTTATT
 CTTCTTTCAG TTGGT

GeneView

GeneView via analysis of contig annotation: PLA2G4A phospholipase A2, group IVA (cytosolic, calcium-dependent)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_004487->NM_024420

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_004487->NM_024420->NP_077734	37387197	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12720579 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838533.2	18974196	158131055	minus	C	alt_assembly_8	HuRef	HuRef	view	255
1	NW_926128.1	25261984	160007225	plus	G	alt_assembly_1	Celera	Celera	view	255
1	NT_004487.18	37387197	185163466	plus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY552098

dbSNP Blast Analysis
GenBank HTGS Finished:
AL022147.3

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss20418471	PDR90	Global	174	IG	0.011	0.989	1.000	0.006	0.994

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.011+/-0.075	90	90	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .