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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs17556981          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/130
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_001134734.1:c.1312T>C
NM_032884.2:c.742T>C
NM_032884.3:c.742T>C
NP_001128206.1:p.Tyr438His
NP_116273.2:p.Tyr248His
NT_032977.8:g.4639644T>C
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 ss24259830 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17556981 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
ss24259830PERLEGEN|afd1008469fwd/BC/Tgtgacggttgctgacaagaacaacccgaagacacagggaatgttttcactccacactttc08/10/0410/21/04123Genomicunknown
ss74900921ILLUMINA|ILMN_Human_1M_rs17556981fwd/BC/Tgtgacggttgctgacaagaacaacccgaagacacagggaatgttttcactccacactttc08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17556981|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 TGTCCTGGCC TCTCCCTGCC TCCATCACTG ACCCGCTTTG CCTCTCCTGT GACTTGCAGT
 TAACGCACCT GTGACGGTTG CTGACAAG
 AACAACCCGA AG
 Y
 ACACAGGGAA TG
 TTTTCACTCC ACACTTTCCT ACAGCCATGA CCTCAGCAAC CCTGAACCAG CCACTCTGGC
 TCAACCTGAA CTATCCACCT CCACCAGT

  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_000001.5
dbSNP Blast Analysis
UniGene Cluster ID
194610

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/T
 T/T
 HWP C
 T
ss24259830 AFD_EUR_PANEL European 46 IG 0.043 0.957 1.000 0.022 0.978
AFD_AFR_PANEL African American 44 IG 1.000 1.000
AFD_CHN_PANEL Asian 42 IG 1.000 1.000
HapMap-CEU European 116 IG 1.000 1.000
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
Concordant Genotype Total Sample C/T T/T
ss24259830 586 318
RefSNP Genotype Summary Total Individual C/T T/T
rs17556981 581 318
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
162 ss24259830 C/T PERLEGEN AFD_EUR_PANEL NA07019 71_IND_CHR_1
162 ss24259830 T/T CSHL-HAPMAP HapMap-CEU NA07019 CEPH1340.02 r27_ch1_CEU_bcm:genotype_0002
Genotype data submitted for596 samples from581 individualsIndividual with multiple genotypes submission:15

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

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Revised: May 25, 2006 1:38 PM .