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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1279138          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_018706.5:c.58C>T
NP_061176.3:p.Leu20Phe
NT_077569.2:g.6473986T>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 ss88098879 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1279138 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
ss2001249KWOK|OVLP-000925-295316byFreqrev/TA/Gcgccccgctcggtctggtagccacgccagagagagggagagcccggccgaggccccgtcg10/06/0010/25/0687Genomic99 %
ss2560952SC_JCM|AC073160.2_57536byFreqfwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg11/03/0004/07/0489Genomicunknown
ss6550101WI_SSAHASNP|NT_008705.13_6473268fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg02/12/0310/10/03111Genomicunknown
ss12069246WI_SSAHASNP|chr10.NT_077569.2_6473986fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg07/04/0310/10/03116Genomicunknown
ss23593505PERLEGEN|afd4109355byFreqfwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg08/10/0409/13/04123Genomicunknown
ss28510364MGC_GENOME_DIFF|BC002477x29800963-T6473986Cfwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg08/25/0408/25/04126cDNAunknown
ss28510539MGC_GENOME_DIFF|BC007955x29800963-T6473986Cfwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg08/25/0408/25/04126cDNAunknown
ss77644335HGSV|Cor12156_SNV_20070510.chr10_12151096fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg10/09/0710/14/07129Genomicunknown
ss83617641HGSV|Cor18555_SNV_20070510.chr10_12151096fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg11/27/0712/05/07130Genomicunknown
ss85652660HGSV|Cor19129_SNV_20070510.chr10_12151096fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg12/06/0712/09/07130Genomicunknown
ss88098879BCMHGSC_JDW|JWB-0236768fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg02/26/0802/27/08129Genomicunknown
ss106657089BGI|BGI_rs1279138fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg09/16/0806/17/09130Genomicunknown
ss1153685391000GENOMES|NA19240_2008_12_16_2073548_chr10_12151096fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg12/18/0812/19/08130Genomicunknown
ss119036491ILLUMINA-UK|NA18507_000018750_NCBI36.1_chr10_12151096fwd/BC/Tcgacggggcctcggccgggctctccctctctctggcgtggctaccagaccgagcggggcg01/21/0901/22/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1279138|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCTGGGCGTC GCTTCGCTGT GAGTGCCGCT GCCACGGATT GGCTTCCAGG GTCCGGCCCG
 TCGGCCAATC AGGCGCGGGG GCGTTGTCTG GGGGCGGGGC TCCGGCCGCC TCTGACGAGT
 CCCGGATTTA CCAGGGCCGG TGGGATCCCC TCGGGCTCCC GCCTTAGCAT GCTGGCCGGG
 ACATCTGGTG AACATGGCCT CTGCTACTGC GGCAGCAGCA CGACGGGGCC TCGGCCGGGC
 TCTCCCTCTC
 Y
 TCTGGCGTGG CTACCAGACC GAGCGGGGCG TTTACGGCTA CCGGCCGAGG AAGCCCGAGA
 GCCGCGAGCC CCAGGGCGCC CTGGAGCGCC CCCCAGGTCG GGGATGGGGC CCGGGCGGTG
 GGAGCGGGGG CTGGGACGCA GAAGCCTCCC CTGGCCGATT TGCGGTGGGG TGTCGGGGTC
 GGGGAACCGG CTGCCGGCCT GAACGCGCGG CCGGTGGGGA GGAGGGGGAG GTGAGGGGAG
 CAGAGGGTAG

  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_077569 AC027507 AC073160.2 BC002477 BC007955
dbSNP Blast Analysis
UniGene Cluster ID
104980

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss2001249 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.667 0.317 0.017 0.479 0.825 0.175
EURAME 32 GF 1.000 1.000
AFRAME 32 GF 0.188 0.812 0.752 0.094 0.906
ss23593505 AFD_EUR_PANEL European 46 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.826 0.174 0.655 0.913 0.087
AFD_CHN_PANEL Asian 44 IG 1.000 1.000
ss2560952 SC_12_A Asian 18 IG 1.000 1.000
SC_12_AA African American 22 IG 0.727 0.273 0.655 0.864 0.136
SC_12_C European 14 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.230+/-0.249 609 478 23 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .