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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1129332          
refSNP ID: rs1129332
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/129
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_007033.3:c.*1647C>T
NT_004350.18:g.1814839C>T
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 ss61708532 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1129332 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
ss1518880LEE|257623fwd/TA/Gcacaagatggaacttgagatttcctgaagccagtgttaaaatgcctcgagggcgtgtgcc09/13/0010/10/0386cDNAunknown
ss16437626CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_004350.16_313872rev/BC/Tggcacacgccctcgaggcattttaacactggcttcaggaaatctcaagttccatcttgtg02/17/0403/04/04120Genomicunknown
ss20561188SSAHASNP|WGSA-200403-chr1.chr1.NT_004350.16_313872rev/BC/Tggcacacgccctcgaggcattttaacactggcttcaggaaatctcaagttccatcttgtg03/18/0403/18/04121Genomicunknown
ss44105721ABI|hCV184630byFreqfwd/TA/Gcacaagatggaacttgagatttcctgaagccagtgttaaaatgcctcgagggcgtgtgcc07/18/0511/03/06126Genomicunknown
ss61708532SI_EXO|NT_004350.17_716555rev/BC/Tggcacacgccctcgaggcattttaacactggcttcaggaaatctcaagttccatcttgtg07/11/0608/17/06127Genomicunknown
ss75000071ILLUMINA|ILMN_Human_1M_rs1129332fwd/TA/Gcacaagatggaacttgagatttcctgaagccagtgttaaaatgcctcgagggcgtgtgcc08/28/0708/29/07129Genomicunknown
ss87165663BCMHGSC_JDW|JWB-0001622rev/BC/Tggcacacgccctcgaggcattttaacactggcttcaggaaatctcaagttccatcttgtg02/26/0802/26/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1129332|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129
 GTCGGAAGCA TTTGGCACAC ACACCTTCAA TACACGTCAA GGTCGCTTCC AGTTTTAGAA
 AACAGAAATC TGCATCTCAG CCTGAGACGC ACAGAGAGGT CTCTTCCTGA CCCAGACGCA
 CTCACGAGCC AGGTCCTGGG GGTATGGGGG CTGCCAGGGG CGCCCGAGCC CTCTCCTGGG
 GGGCCTGCTG GGCAGGCGAC CTGCTGACCC ACGGTCACTG CTGTGTTCAG CCCCTCAGCT
 CGGCCCCAGC CTATTTCCCG CCTCCATTTG ATGTTTCCAG GTTTTCAAAA CTGCATTTAA
 CCTGCGCCAG AGAGTTCACC GTAGGCATCT TTAATAAACT AACTCCAGCA AAATGTGGGT
 ACGTTACTAA CACAAGATGG AACTTGAGAT TTCCTGAAGC
 R
 CAGTGTTAAA ATGCCTCGAG GGCGTGTGCC ACATTTCCCT GCTGACGTAA AACACCTGGC
 CAGCAGGACC GGCTTCCGGC AAAGACCCGC GCAAACCATG TCTTGCTGTT TGACTTACTT
 AGGAATGAGG ATGACCCTGT ATTCCTGGGT TAGTCAAGGT CAGCTTGCCA GAGACGGAGG
 AGGGCGGGGG GGCCGTGACC CTCTAGACTG GGAGGACCAC CAGGAGAGGC ACTGGGGGCT
 GCGGCCGGGT GGGCAGATGC CGCCGTGGCT CCATCCATCA GCACCCAGTC CTTTGCTTCA
 CTGTGCTCTG GCCAAGCGCG TGCGACTTCC TGTCACACCT TAGGCCTGAG CGCTTATTAA
 GAAAACAGTA TGAAAAATGA CAAACACTCC TGTCCACAGT

  GeneView back to top
GeneView via analysis of contig annotation: RER1 RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: PEX10 peroxisomal biogenesis factor 10
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_004350->NM_007033
function
referenceNT_004350->NM_002617
function
referenceNT_004350->NM_153818
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_004350->NM_007033->1814839forward24293' UTR
referenceNT_004350->NM_002617->NP_0026081814839reverse3' near gene
referenceNT_004350->NM_153818->NP_7225401814839reverse3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1129332 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_921350.1250496250496plusAalt_assembly_1CeleraCeleraview400
1NW_001838585.115956721614919minusCalt_assembly_8HuRefHuRefview400
1NT_004350.1818148392326070minusCref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004350.17 Hs.247220
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank HTGS Finished:
NM_007033.3 AL513477.21

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPA
G
ss44105721AoD_African_American 90AF 0.140 0.860
AoD_Caucasian 92AF 0.330 0.670
AoD_Chinese 90AF 0.370 0.630

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.404+/-0.1970000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .