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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs12657663          
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_001745.2:c.232G>A
NP_001736.1:p.Val78Ile
NT_034772.5:g.36491825G>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 ss20251821 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12657663 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
ss20251821CSHL-HAPMAP|CSHL-HuFF-200402.chr5.NT_034772.5_36491825byFreqfwd/TA/Gcaggacagtgataaactgaactccctcagcttccttccgtttcaaagcgagtagtgctgg02/21/0405/17/04120Genomicunknown
ss65730643ILLUMINA|Human1-rs12657663fwd/TA/Gcaggacagtgataaactgaactccctcagcttccttccgtttcaaagcgagtagtgctgg10/10/0610/10/06127Genomicunknown
ss65835314KRIBB_YJKIM|KHS11106byFreqfwd/TA/Gcaggacagtgataaactgaactccctcagcttccttccgtttcaaagcgagtagtgctgg10/17/0612/16/06127Genomicunknown
ss68950527PERLEGEN|PGP04775652byFreqfwd/TA/Gcaggacagtgataaactgaactccctcagcttccttccgtttcaaagcgagtagtgctgg01/30/0703/31/08127Genomicunknown
ss74813031AFFY|SNP_M-288919fwd/TA/Gcaggacagtgataaactgaactccctcagcttccttccgtttcaaagcgagtagtgctgg08/09/0708/09/07128Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12657663|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=128
 TTTAATGCAG AATCGGTATT TATTTATTTT GATGCAGAGG CTGCTGAGTT CTAGCTGCAA
 CAGCATATTT TAAAACATAA ACATGTAAGG TGTTTGCCAG TATGGAATAA ATACATAAGG
 CTTTTACATT TCTTTTCTCA GAAGAAGAAA GTCAAACAAA ATCAAAGCAG CAGGACAGTG
 ATAAACTGAA CTCCCTCAGC
 R
 TTCCTTCCGT TTCAAAGCGA GTAGTGCTGG GTGATTCAGT CAGTACAGGA ACAACTGACC
 AGCAGGGTGG TGTGGCCGAG GTAAAGGGGA CCCAACTGGG AGACAAATTG GACTCGTTCA
 TTAAACCACC TGAGTGCAGT AGTGATGTCA ACCTTGAGCT CCGGCAGCGG AACAGAGGGG
 ACCTGACAGC GGACTCGGTC

  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_034772
dbSNP Blast Analysis
UniGene Cluster ID
529846

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss20251821 HapMap-CEU European 120 IG 0.183 0.817 0.439 0.092 0.908
HapMap-HCB Asian 90 IG 0.089 0.378 0.533 0.752 0.278 0.722
HapMap-JPT Asian 88 IG 0.136 0.477 0.386 1.000 0.375 0.625
HapMap-YRI Sub-Saharan African 118 IG 0.068 0.932 1.000 0.034 0.966
ss65835314 KHP1 178 AF 0.079 0.494 0.427 0.251 0.326 0.674
ss68950527 HapMap-CEU European 120 GF 0.183 0.817 0.092 0.908
HapMap-HCB Asian 90 GF 0.089 0.378 0.533 0.278 0.722
HapMap-JPT Asian 88 GF 0.136 0.477 0.386 0.375 0.625
HapMap-YRI Sub-Saharan African 120 GF 0.067 0.933 0.033 0.967

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.322+/-0.239 525 409 270 0

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

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Revised: May 25, 2006 1:38 PM .