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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs12134870          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
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_001126.2:c.535C>T
NP_001117.2:p.Leu179Phe
NT_004836.17:g.9345090G>A
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 ss18277463 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12134870 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
ss18277463SC_SNP|SC-CHR1_NA07340-200402.chr1.NT_004836.15_9250665fwd/TA/Gcaaagtcagaaacaaggtcgcacatcctgatccactccgagcagctttggacgaataaac02/20/0403/04/04120Genomicunknown
ss68799866PERLEGEN|PGP04751127fwd/TA/Gcaaagtcagaaacaaggtcgcacatcctgatccactccgagcagctttggacgaataaac01/30/0701/30/07127Genomicunknown
ss74860882ILLUMINA|ILMN_Human_1M_rs12134870fwd/TA/Gcaaagtcagaaacaaggtcgcacatcctgatccactccgagcagctttggacgaataaac08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12134870|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129
 AGAATGTAAT AAAAATAACT TTAATATTTC AAACCTAAAA AAGCCAACCA CCACTATTTA
 ACTAGAATAC CGACTGTATC ATTTTGCACC CTAGATTTTA AAAAAAATCA AAAAATGCAT
 TCATTCCTTC CATTTTGAAA CACAAGTTAG TTACCTCTCA GAGAAGCCAT CAAAGTCAGA
 AACAAGGTCG CACATCCTGA
 R
 TCCACTCCGA GCAGCTTTGG ACGAATAAAC TGGGCCAATG CCCTTTTTTG TTGTACCCAA
 ACTTAAAAAC AAATCCAAAC AAGCTTTAAG TCAGACAAGA AAGATGTAGG TCTCCTGGTC
 AGATCATTGC AGTGAATAAA GTTACATATG ACTATTTTCT GTTTATGTTA TTTCTTGCTA
 AGTATATGTT CATAATCCTA

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_004836
dbSNP Blast Analysis
UniGene Cluster ID
498313

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/G
 G/G
 HWP A
 G
ss18277463 HapMap-CEU European 120 IG 0.017 0.983 1.000 0.008 0.992
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
ss68799866 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000
Concordant Genotype Total Sample A/G G/G
ss18277463 779 8 663
RefSNP Genotype Summary Total Individual A/G G/G
rs12134870 780 8 663
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
158 ss18277463 G/G CSHL-HAPMAP HapMap-CEU NA12145 CEPH1334.11 r27_ch1_CEU_illumina:human_1m_beadchip 1546469
Genotype data submitted for780 samples from780 individualsIndividual with multiple genotypes submission:0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterwithHapMapFreq UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .