NCBI

NLM

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
Spacer gif
BUILD 129
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs279834          
refSNP ID: rs279834
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_000807.1:c.188-3600C>G
NT_006238.10:g.6040265G>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 ss1894988 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs279834 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
ss363144KWOK|OVLP-000621-145263fwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca06/30/0010/10/0379Genomic99 %
ss537029SC_JCM|AC015523.3_8771fwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca07/12/0010/10/0380Genomicunknown
ss1100937KWOK|OVLP-000804-194285fwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca09/02/0010/10/0386Genomic99 %
ss1423124TSC-CSHL|TSC0283183fwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca09/06/0010/10/0386Genomic95 %
ss1894988KWOK|OVLP-000925-347509byFreqfwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca10/06/0005/16/0489Genomic99 %
ss5519045TSC-CSHL|TSC0658902fwd/BC/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca09/21/0210/10/03108Genomicunknown
ss44525618ABI|hCV7537262fwd/C/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca07/19/0507/19/05126Genomicunknown
ss81024074HGSV|Cor18555_SNV_20070510.chr4_46179227fwd/C/Gttactagtcatgaggaaaagatgcccatcattgtgaaggcagagtccatttccattgaca11/27/0711/27/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs279834|allelePos=914|totalLen=1114|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 ATGTATGTTA CAGAGTAAAC AAGTTAATTT ACAGTCTGGT GGCAACCTGA GTCTCTGTGC
 ATTTTAGGTA CCATGATTCA CTCTTCAGTC TTGATCACTC tttttttgtt gtttttgttc
 tttagatgga atttcgctct tattgcccag gctggagtgc agtggtgcga tctcagctca
 ccgcaacctc tgcctccagg gttcaagtga ttctcctgcc tcagcctccc aagtaactgg
 gactacagac gcacaccacg tccagctagt ttttgtattc ttagtagaga tggggtttca
 ccatgttggc caggctggtc tcaaactcct gacctcaggt gatccaccca cctcggcctc
 ccaaagcact gggattacag gcatgagcca ccgtgcctgg ccCTGATCAC TCTTAGTTGa
 cacaccaaag tctgtcctga ctcagagcct tcaaaatggc cattatctcg cattttctct
 ttggttaact gctcctttgc atttaagtct cagtttaaat ggtctctctt cagagcagga
 gttcacaaac ctctatgtaa tgtaagccct cttctctcat ttttgctctc tgacactttc
 tttttatggg acctttcaac tttgccttta ttttaatgcc ttaatatatt cttcttgctt
 tttgtcttgt gtttggtctg tctccccatc caggatttaa gctccacaaa gaacagggac
 tgcactattt ctgttcacta ttatgtcatg agggcttact acaatgtcta tcacatgtta
 catgctgtat gtttgAACAA ATTATTTCTC ATTTTAATTC ATGTAGAATA TCGATCTTTT
 TCCAAAATAT ATCATCAACT TTAAAAATGG TCATGCATAG CTGTTACTAG TCATGAGGAA
 AAGATGCCCA TCA
 S
 TTGTGAAGGC AGAGTCCATT TCCATTGACA AAGGCAGGTT GAGAGTATAA GTAATAGGCT
 TCCAGTGAAG TAACAAAGCT GAGCAAAGGG AAAGAATGTA CTTGAAGACA GCACTGATTC
 ACTGCAAACC AAAATTGAAG TCTGAACAGT TAAGCAGCTC CTAGCAGAAA TATCCACCAG
 CTAAATAATG GTTTACCATT

  GeneView back to top
GeneView via analysis of contig annotation: GABRA2 gamma-aminobutyric acid (GABA) A receptor, alpha 2
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_006238->NM_000807
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_006238->NM_000807->NP_0007986040265reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs279834 maps exactly once on NCBI human chromosome 4
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
4NW_001838903.1603479645656361plusGalt_assembly_8HuRefHuRefview913
4NT_006238.10604026546033056plusGref_assemblyreferencereferenceview913
4NW_922073.13691404246787300plusGalt_assembly_1CeleraCeleraview913

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
AC015523 AC013490 AC015523.3
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss1894988CEPH 184AF 0.420 0.580
HapMap-CEUEuropean 106IG 0.283 0.415 0.302 0.150 0.491 0.509
HapMap-HCBAsian 86IG 0.256 0.581 0.163 0.273 0.547 0.453
HapMap-JPTAsian 86IG 0.209 0.465 0.326 0.752 0.442 0.558
HapMap-YRISub-Saharan African 112IG 0.018 0.268 0.714 1.000 0.152 0.848

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.478+/-0.10327021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP, NCBI
UNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .