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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1131442          
refSNP ID: rs1131442
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:Not available
Clinical Association:unknown
HGVS Names
NM_002460.1:c.*58G>A
NT_034880.3:g.347656G>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 ss71642571 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1131442 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
ss1526117LEE|432899fwd/TA/Gtccttttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct09/13/0010/10/0386cDNAunknown
ss22436335SSAHASNP|WGSA-200403-chr6.chr6.NT_034880.3_347656fwd/TA/Gttcctttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct03/21/0403/21/04121Genomicunknown
ss42877287ABI|hCV1576159byFreqfwd/TA/Gttcctttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct07/18/0511/03/06126Genomicunknown
ss71642571SI_EXO|NT_034880.3_347656byFreqfwd/TA/Gttcctttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct05/07/0703/31/08127Genomicunknown
ss81960072HGSV|Cor19240_SNV_20070510.chr6_352656fwd/TA/Gttcctttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct11/30/0712/01/07130Genomicunknown
ss93362978BCMHGSC_JDW|JWB-2085340fwd/TA/Gttcctttttttttttttttttttgatacgggatacggggtcttgctctgtctcccaggct02/26/0803/04/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1131442|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GTTTTTTTAC ATGTTGATCT ATGGAAGGAC TAACCAAAAA ATTGCTTCTT TAGATGGCTC
 CAAATATGAA ATGTTTTGAT GTGTTCTAGG ATGTAACTTT GGGCTTTACG TTACTGTCTC
 CTTAGAATCT GAGTGCTGTT TAATAGTGAG CCAGTTGCAG GATATCTCAG TAATGTCTTT
 TTAAAATCTC TTATTAAAGG TAGAACCTCT GCTAGCCAGA CAACTATATT ATTTTGCTCA
 ACAAAACAGT GGACATTTCC TGAGGGGCTA CGATTTACCA GAACACATCA GCAATCCAGA
 AGATTACCAC AGATCTATCC GCCATTCCTC TATTCAAGAA TGAAAAATGT CAAGATGAGT
 GGTTTTCTTT TTCCTTTTTT TTTTTTTTTT TTTGATACGG
 R
 GATACGGGGT CTTGCTCTGT CTCCCAGGCT GGAGTGCAGT GACACAATCT CAGCTCACTG
 TGACCTCCGC CTCCTGGGTT CAAGAGACTC TCCTGCCTCA GCCTCCCTGG TAGCTGGGAT
 TACAGGTGTG AGCCACTGCA CCCACCCAAG ACAAGTGATT TTCATTGTAA ATATTTGACT
 TTAGTGAAAG CGTCCAATTG ACTGCCCTCT TACTGTTTTG AGGAATTCAG AAGTGGAGAT
 TTCAGTTCAG CGGTTGAGGA GAATTGCGGC GAGACAAGCA TGGAAAATCA GTGACATCTG
 ATTGGCAGAT GAGCTTATTT CAAAAGGAAG GGTGGCTTTG CATTTCTTGT GTTCTGTAGA
 CTGCCATCAT TGATGATCAC TGTGAAAATT GACCAAGTGA

  GeneView back to top
GeneView via analysis of contig annotation: IRF4 interferon regulatory factor 4
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_034880->NM_002460
svfunction
HuRefNW_001838972->NM_002460
svfunction
CeleraNW_922984->NM_002460
svfunction
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_034880->NM_002460->347656forward15193' UTR
HuRefNW_001838972->NM_002460->3374572reverse15193' UTR
CeleraNW_922984->NM_002460->31395forward15193' UTR

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1131442 maps exactly once on NCBI human chromosome 6
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
6NW_001838972.23374572280292minusTalt_assembly_8HuRefHuRefview400
6NT_034880.3347656352656plusGref_assemblyreferencereferenceview400
6NW_922984.1313951636139plusGalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U63738 Hs.82132
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
NC_000006.10 AC139253.1 AC139288.1 AC139289.1 AC139466.1 AC139481.2 AC139823.1 AC141063.1 AC141261.1 AC141271.1 AC141295.1 AC141309.1 AC141600.1 AC141603.1 AC143325.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss42877287HapMap-CEUEuropean 118IG 0.102 0.525 0.373 0.317 0.364 0.636
HapMap-HCBAsian 84IG 0.214 0.738 0.048 0.001 0.583 0.417
HapMap-JPTAsian 86IG 0.209 0.558 0.233 0.479 0.488 0.512
ss71642571HapMap-CEUEuropean 118IG 0.102 0.525 0.373 0.364 0.636
HapMap-HCBAsian 84IG 0.214 0.738 0.048 0.583 0.417
HapMap-JPTAsian 86IG 0.209 0.558 0.233 0.488 0.512

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.498+/-0.03518015000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .