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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2578652          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_198141.2:c.1329T>A
NP_937784.2:p.Asp443Glu
NT_010194.16:g.13409088T>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 ss3622463 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2578652 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
ss3622463SC_JCM|AC012651.6_137993byFreqfwd/BA/Ttttggccttcacatatactgagtagtcaggtcaatcttgatgtggggatcactgatgacc09/24/0110/21/04100Genomicunknown
ss69174803PERLEGEN|PGP04757501byFreqrev/A/Tggtcatcagtgatccccacatcaagattgacctgactactcagtatatgtgaaggccaaa01/30/0708/14/07127Genomicunknown
ss74820003AFFY|SNP_M-322040fwd/BA/Ttttggccttcacatatactgagtagtcaggtcaatcttgatgtggggatcactgatgacc08/09/0708/09/07128Genomicunknown
ss76770298AFFY|AFFY_6_1M_SNP_A-8631652rev/A/Tcccacatcaagattgacctgactactcagtat08/28/0708/30/07130Genomicunknown
ss86239414CORNELL|hCV15898502rev/A/Tggtcatcagtgatccccacatcaagattgacctgactactcagtatatgtgaaggccaaa01/21/0801/21/08129Genomicunknown
ss104875374KRIBB_YJKIM|KHS1267692fwd/A/Ttttggccttcacatatactgagtagtcaggtcaatcttgatgtggggatcactgatgacc07/10/0807/10/08130Genomicunknown
ss1087697461000GENOMES|CEU.trio.12.15.2008_3152684_chr15_40405823rev/A/Tggtcatcagtgatccccacatcaagattgacctgactactcagtatatgtgaaggccaaa12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2578652|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=130
 AGCTAGAGGA GCAAGAGACA TCTACAAGGG AGCAGAATGA TGACCACGCA GCCTTCATTA
 ATTGGGACAG AACATGTGGA AATAATAAGT GTATAAAGTG ATTTCATACC TGGCCAACAC
 ACCCCTTCAA AGTCTTCCCC TTCCTGATTC TTCACAAAGA AGCCCTGATC TTTGGCCTTC
 ACATATACTG AGTAGTCAGG
 W
 TCAATCTTGA TGTGGGGATC ACTGATGACC ACAAGCTGTC AGGACATGAA GGTTTGGAGG
 TCTCATCAGT TTTATGTAAG ACAAATGTTC ACGTATATGT TTTCGCCATA GTTTGGGGGT
 TCAATTTTTA CAAACAACTA CAACTAGTAT TGAAATATTT CAGACAAaaa aacaaaaaca
 aaaacaaaaa ATAAATATTT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NC_000015.8 AC022468
dbSNP Blast Analysis
UniGene Cluster ID
143261

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/T
 T/T
 HWP A
 T
ss3622463 HapMap-CEU European 116 IG 0.741 0.241 0.017 1.000 0.862 0.138
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 86 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 116 IG 1.000 1.000
ss69174803 HapMap-CEU European 120 GF 0.750 0.233 0.017 0.867 0.133
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000
Concordant Genotype Total Sample A/A A/T T/T
ss3622463 1121 873 60 1
ss69174803 269 1 22 246
RefSNP Genotype Summary Total Individual A/A A/T T/T
rs2578652 1122 874 62 247
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
538 ss3622463 A/A CSHL-HAPMAP HapMap-CEU NA12753 CEPH1447.02 r27_ch15_CEU_affymetrix:genomewidesnp_6.0
538 ss69174803 T/T CSHL-HAPMAP HapMap-CEU NA12753 CEPH1447.02 chr15-HapMap-CEU
Genotype data submitted for1122 samples from1122 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .