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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs13034312          
refSNP ID: rs13034312
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/129
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_005270.3:c.149-14410G>A
NT_022135.15:g.10378449G>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 ss44137285 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13034312 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
ss21747703SSAHASNP|WGSA-200403-chr2.chr2.NT_022135.13_10378269fwd/TA/Ggggcggggcaccggcctcacccacagaatccaagtaaccctcctacgattctgggaacgt03/20/0403/20/04121Genomicunknown
ss44137285ABI|hCV1291257fwd/TA/Ggggcggggcaccggcctcacccacagaatccaagtaaccctcctacgattctgggaacgt07/18/0507/18/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs13034312|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=126
 AACACGGCTT GCCCGGTGTT TCTCCACGGT CCTGCCGCAC TGCCCCTCAT GACCCCGGCA
 TGGGCTTTGC TTTCTGCGGA CCCTCTTATT TGTCGAAGAT CTCGGGAGTC CACACACCCA
 CTCCCGTGTC TGGGAACACT CCAAGCTTAT CAAGAACGCA GCGGGCAGCA ATCCAGGGCA
 GAACAAGGGA GGTGCTGTCG ACCAGCTCTG CGCGGAGAGG TCAAGGGTGT GGAAGGGTGG
 GGAGAGAGGC ACAGGCTGAC TTAATCCCTT GGGCGGGGCA CCGGCCTCAC CCACAGAATC
 R
 CAAGTAACCC TCCTACGATT CTGGGAACGT TTGTGAGTTA AATGAATGGA AGGGAGGGAG
 GAAAGGAGGG AAGAAAAATA ACTGTGTTTT CATCAGTAAA TGTAAGCGAC CAAATAGAAG
 TCTGTAGGAA GCTAAGATTC AGAGGTGAGG AAGGACTGAG GTTTGGGGAG AATTCTCATC
 ACCATATTTT GTGTATTGAT GGGACTTTTA CTAAGCTAGA CTAGAATTCC GAAGCAGTGG
 AAAGTCAATA ATGATAACGA GTTAGGCCTG AGCTGTTCAG TAGGGTAGCC GCGAGCTGTG

  GeneView back to top
GeneView via analysis of contig annotation: GLI2 GLI-Kruppel family member GLI2
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_022135->NM_005270
function
HuRefNW_001838848->NM_005270
function
CeleraNW_921507->NM_005270
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_022135->NM_005270->NP_00526110378449forwardintron
HuRefNW_001838848->NM_005270->NP_005261520110forwardintron
CeleraNW_921507->NM_005270->NP_0052617268898forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs13034312 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
2NW_001838848.1520110113993042plusAalt_assembly_8HuRefHuRefview300
2NW_921507.17268898114995526plusGalt_assembly_1CeleraCeleraview300
2NT_022135.1510378449121386997plusGref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022135
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
HWPG
ss44137285HapMap-CEUEuropean 118IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 88IG 1.000 1.000
HapMap-YRISub-Saharan African 116IG 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
withHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .