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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs9820762          
refSNP ID: rs9820762
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_024524.3:c.560+501G>A
NT_005535.16:g.120814C>T
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 ss44426479 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9820762 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
ss13653170BCM_SSAHASNP|chr3.NT_005535.15_120814fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa11/05/0310/25/06119Genomicunknown
ss44426479ABI|hCV429961byFreqfwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa07/18/0511/03/06126Genomicunknown
ss66663650ILLUMINA|HumanHap300v1.1_rs9820762fwd/TC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa11/09/0611/09/06127Genomicunknown
ss67948277ILLUMINA|HumanHap550v1.1_rs9820762fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa11/14/0611/15/06127Genomicunknown
ss68061323ILLUMINA|HumanHap650Yv1.0_rs9820762fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa11/14/0611/15/06127Genomicunknown
ss68887493PERLEGEN|PGP04857279byFreqfwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa01/30/0703/31/08127Genomicunknown
ss71626125ILLUMINA|HumanHap650Yv3.0_rs9820762fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa04/23/0704/23/07127Genomicunknown
ss75543786ILLUMINA|ILMN_Human_1M_rs9820762fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa08/28/0708/29/07129Genomicunknown
ss76705840AFFY|AFFY_6_1M_SNP_A-8567150fwd/BC/Tatttatctttaacatagcaatacactggtgta08/28/0708/30/07129Genomicunknown
ss79304899ILLUMINA|HumanHap300v2.0_rs9820762fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa04/18/0711/18/07130Genomicunknown
ss80667225HGSV|Cor18507_SNV_20070510.chr3_195658619fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa11/23/0711/26/07130Genomicunknown
ss84856765KRIBB_YJKIM|KHS830833fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa12/04/0712/08/07130Genomicunknown
ss86183963HGSV|Cor18517_SNV_20070510.chr3_195658619fwd/BC/Taatttcaaagtggcatttatctttaacatagcaatacactggtgtatttttatgatttaa12/06/0712/11/07130Genomicunknown
ss98290135ILLUMINA|HumanHap550v3.0__rs9820762rev/TA/Gttaaatcataaaaatacaccagtgtattgctatgttaaagataaatgccactttgaaatt04/20/0703/31/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9820762|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TTTTTGCAAG AAGCCAAATA AATTTGAGGG ATCTTATTTT TTTTTTAATA TTGCACTAAC
 AGTGTTTAGT TCAAAACATT GTACATTCGA CTTTAAAAGA AAATGCTTTT AAAGTTTAAA
 TGTTTCCACT TAATTCCTTA TGTTACAATA GTATTTTCTA TATGATAGAG TAATTCTAGA
 CTTTTATGAA ATGTAAGTCT AAATGAGTGA ATTTTATGTT CTACCCCTTT GAAAGAACAT
 GTTACAGAAC TATAAGAAAA TTTCTTATTG AATTTCAAAG TGGCATTTAT CTTTAACATA
 Y
 GCAATACACT GGTGTATTTT TATGATTTAA CAAGGAATAA CACAATGAAG GAGATTATGT
 CTCCCAATTT ACAATCTTTC ATTACGGTGA ATTTGAACTC ATGCTTGTAT TTCAGAAAAT
 CTAAGGTGCT ATCAATTGTA AGGCATACCA TTATTATATG ATCAAGAAAG ATAAAAATGC
 TATCAAGAAC GACACTTCAC CAACTCTATG ACACATCCCA ATCTCAGAGA TGTTAAAAGG
 TGGAAAAACG TGCACCTGGG AACTGATGAA ATATGGTATA ATTTCAGGGA TACCAACTTC

  GeneView back to top
GeneView via analysis of contig annotation: ATP13A3 ATPase type 13A3
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_005535->NM_024524
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_005535->NM_024524->NP_078800120814reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs9820762 maps exactly once on NCBI human chromosome 3
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
3NW_001838885.21163803191557195minusAalt_assembly_8HuRefHuRefview300
3NW_921807.1100778351192592681plusCalt_assembly_1CeleraCeleraview300
3NT_005535.16120814195658611plusCref_assemblyreferencereferenceview300

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_005535
dbSNP Blast Analysis
GenBank HTGS Draft:
AL359264.8

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss44426479HapMap-CEUEuropean 120IG 0.650 0.300 0.050 0.655 0.800 0.200
HapMap-HCBAsian 82IG 0.463 0.512 0.024 0.720 0.280
HapMap-JPTAsian 84IG 0.571 0.405 0.024 0.774 0.226
HapMap-YRISub-Saharan African 120IG 0.217 0.467 0.317 0.752 0.450 0.550
ss68887493HapMap-CEUEuropean 120GF 0.650 0.300 0.050 0.800 0.200
HapMap-HCBAsian 90GF 0.511 0.467 0.022 0.744 0.256
HapMap-JPTAsian 90GF 0.556 0.422 0.022 0.767 0.233
HapMap-YRISub-Saharan African 120GF 0.233 0.450 0.317 0.458 0.542
Concordant GenotypeTotal SampleC/CC/TT/T
ss4442647926711910932
ss6888749326712211332
RefSNP Genotype SummaryTotal IndividualC/CC/TT/T
rs982076227012211332
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
5174ss44426479C/TCSHL-HAPMAPHapMap-HCBNA18571CH18571r23_ch3_HCB_illumina:infinium_genotyping_2.0.0412668
5174ss68887493C/CCSHL-HAPMAPHapMap-HCBNA18571CH18571chr3-HapMap-HCB
5201ss44426479C/TCSHL-HAPMAPHapMap-JPTNA18948JA18948r23_ch3_JPT_illumina:infinium_genotyping_2.0.0412668
5201ss68887493C/CCSHL-HAPMAPHapMap-JPTNA18948JA18948chr3-HapMap-JPT
5240ss44426479C/TCSHL-HAPMAPHapMap-YRINA18504YOR005.03r23_ch3_YRI_illumina:golden_gate_1.0.0412668
5240ss68887493C/CCSHL-HAPMAPHapMap-YRINA18504YOR005.03chr3-HapMap-YRI
Genotype data submitted for270 samples from270 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .