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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6142637          
refSNP ID: rs6142637
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_002657.3:c.260+116C>T
NT_028392.5:g.985698G>A
Links

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 ss8475139 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6142637 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
ss8475139SC_SNP|NT_028392.4_985698fwd/TA/Gcaactgtttggcattcagggtatacttgtagacaaattaacctccactcttctgccacag04/17/0310/10/03114Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6142637|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=114
 AGCCACACcc ccatatctac aaaaaattaa aaacaaccag gtgcggtggt tcaagcctgt
 aatcctagtt acctgggaga atgagtcaag agaatcactt gagcccagga attggaggct
 gcagtgagct gattgcacca ctgtactcta gcctggatga cagagcaaga ctcCCATTTC
 TTaaaaaaac aaacaaacaa acaaacaaaA CTCAAGGCTG CCTGACATTG GCACCCAGAT
 CGTCACTAAG AAGGTGTAAG AAggccaggt gcagtggctc acgccagcaa tcccaatact
 ttggggaggc AACCCATCAG ATTCTAGTGT CTGAATCAAG CAATCTGAAT CATTTTTTAG
 TGAGTGACTT CAACTGTTTG GCATTCAGGG TATACTTGTA
 R
 GACAAATTAA CCTCCACTCT TCTGCCACAG ATTAAAAACC CACACTAGGC AGAGTCTCTC
 TGCTTTTTCC CTCTGGGAAC CTCAGGGCAG GAAGAGATAT GAGAGTGTCA CCTACCTATA
 CAGCTTGTAT TTGGAAGCAA AAGCCTTGCC ACAGTGCAGC TGAGGGCAGC TATATGGTCT
 CTGCTCTGGT TGCGGGAGGC TGTGAGGCCT CAGCTTCTCC CCATTTGAGA AAGGTGTTCC
 CGAAATTTCA CATTGGCACT TCACTTGACT CTCCGCCTCC CGGCCCCGAG GCCTGGGAAC
 TAGTTTCCAG CCCACTTCCT CCTCCTGCTT TGCATCTTGA ATCCAGGGGG GGACGCTGGT
 GAAAAATGTG GTCATGGCAA GGCTAATGGC AAAGGGCCAT

  GeneView back to top
GeneView via analysis of contig annotation: PLAGL2 pleiomorphic adenoma gene-like 2
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_028392->NM_002657
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_028392->NM_002657->NP_002648985698reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6142637 maps exactly once on NCBI human chromosome 20
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
20NW_927339.1104906727545958plusGalt_assembly_1CeleraCeleraview400
20NW_001838664.2410187327578117minusCalt_assembly_8HuRefHuRefview400
20NT_028392.598569830253267plusGref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_028392
dbSNP Blast Analysis
GenBank HTGS Finished:
AL121897.32

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
HWPG
ss8475139HapMap-CEUEuropean 114IG 1.000 1.000
HapMap-HCBAsian 88IG 1.000 1.000
HapMap-JPTAsian 86IG 1.000 1.000
HapMap-YRISub-Saharan African 108IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
27021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
with2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .