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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2228007          **clinically associated**
refSNP ID: rs2228007
Organism:human (Homo sapiens)
Molecule Type:cDNA
Created/Updated in build:98/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
Clinical Association:link to VariationViewer
HGVS Names
NM_000535.4:c.1531A>G
NP_000526.1:p.T511A
NT_007819.16:g.5515823T>C
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss3172637 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2228007 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss3172637WIAF-CSNP|WIAF-11623fwd/TA/Ggtggattctgaggggttcagcatcccagaccgggcagtcactgcagcagcgagtatgcgg06/19/0110/10/0398cDNAunknown
ss102662679MMR_WOODS|MMR_PMS2_00139fwd/TA/Ggtggattctgaggggttcagcatcccagaccgggcagtcactgcagcagcgagtatgcgg05/23/0805/28/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2228007|allelePos=151|totalLen=301|taxid=9606|snpclass=1|alleles='A/G'|mol=cDNA|build=130
 GCCATCTCTG ACAAAGGCGT CCTGAGAYCT CAGAAAGAGG CAGTGAGTTC CAGTCACGGA
 CCCAGTGACC CTACGGACAG AGCGGAGGTG GAGAAGGACT CGGGGCAYGG CAGCACTTCC
 GTGGATTCTG AGGGGTTCAG CATCCCAGAC
 R
 CGGGCAGTCA CTGCAGCAGC GAGTATGCGG CCAGCTCCCC AGGGGACAGG GGCTCGCAGG
 AACATGTGGA CTCTCAGGAG AAAGCGCCTR AAACTGACGA CTCTTTTTCA GATGTGGACT
 GCCATTCAAA CCAGGAAGAT ACCGGATGTA

  GeneView back to top
GeneView via analysis of contig annotation: PMS2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_007819->NM_000535
function
HuRefNW_001839002->NM_000535
function
CeleraNW_923217->NM_000535
function
CRA_TCAGchr7v2NT_079592->NM_000535
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_007819->NM_000535->NP_0005265515824reverse1618missenseGAla [A]1511
contig referenceAThr [T]1511
HuRefNW_001839002->NM_000535->NP_000526257961forward2124missenseGAla [A]1511
contig referenceAThr [T]1511
CeleraNW_923217->NM_000535->NP_000526752816forward2124missenseGAla [A]1511
contig referenceAThr [T]1511
CRA_TCAGchr7v2NT_079592->NM_000535->NP_0005266023210reverse1618missenseGAla [A]1511
contig referenceAThr [T]1511

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2228007 maps exactly once on NCBI human chromosome 7
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
7NW_001839002.22579615898715plusAalt_assembly_8HuRefHuRefview150
7NT_007819.1655158245993391minusTref_assemblyreferencereferenceview150
7NT_079592.260232106073210minusTalt_assembly_2CRA_TCAGchr7v2CRA_TCAGchr7v2view150
7NW_923217.17528166709825plusAalt_assembly_1CeleraCeleraview150

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NM_000535
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank STS:GenBank mRNA:
NM_000535.4 XM_001126008.1 BV177873.1 G18338.1 G67276.1 AB103082.1 AB103086.1 BC031832.1 BC093921.1 U14658.1
UniGene Cluster ID
449374 487470

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
HWPA
G
ss3172637WIAF-CSNP-MITOGPOP5multiple 66IG 0.970 0.030 1.000 0.985 0.015

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.030+/-0.118333300

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
bySubmitter
Validated by: PERLEGEN
UNKNOWNYESYES

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Revised: May 25, 2006 1:38 PM .