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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs16870794          
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/G
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_031900.1:c.394G>C
NP_114106.1:p.Gly132Arg
NT_006576.15:g.35009896C>G
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 ss23408898 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16870794 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
ss23408898PERLEGEN|afd3693697byFreqfwd/BC/Gagaagacggtgcttgtatgccacaggcggcgagctgcttttgtgccactgcattcacctt08/10/0409/13/04123Genomicunknown
ss68932150PERLEGEN|PGP03693697byFreqfwd/C/Gagaagacggtgcttgtatgccacaggcggcgagctgcttttgtgccactgcattcacctt01/30/0703/31/08127Genomicunknown
ss74884404ILLUMINA|ILMN_Human_1M_rs16870794fwd/C/Gagaagacggtgcttgtatgccacaggcggcgagctgcttttgtgccactgcattcacctt08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16870794|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=129
 CATTGTACCT TAAGAGGCTC AGGAAGAAGT GCGGCAAGCT TCTCTGCATA TTCATGCATT
 GGAGGGTGGA AGAAGACGGT GCTTGTAT
 GCCACAGGCG GC
 S
 GAGCTGCTTT TG
 TGCCACTGCA TTCACCTTTC TGGATAAGCA GTACAGCAGA GTTACCTGCA CTGCGTGCCA
 CGTCCCTCCT GCACACACCC TGGTCATT

  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_000005.8
dbSNP Blast Analysis
UniGene Cluster ID
34494

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 HWP C
 G
ss23408898 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.652 0.348 0.317 0.826 0.174
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 112 IG 0.857 0.143 0.584 0.929 0.071
ss68932150 HapMap-CEU European 120 GF 1.000 1.000
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 0.800 0.200 0.900 0.100
Concordant Genotype Total Sample C/C C/G
ss23408898 586 306 19
ss68932150 269 253 16
RefSNP Genotype Summary Total Individual C/C C/G
rs16870794 581 307 24
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5136 ss23408898 G/G CSHL-HAPMAP HapMap-YRI NA19132 YOR101.01 r27_ch5_YRI_perlegen:genotyping_1.0.0 2910058
5136 ss68932150 C/G CSHL-HAPMAP HapMap-YRI NA19132 YOR101.01 chr5-HapMap-YRI
Genotype data submitted for596 samples from581 individualsIndividual with multiple genotypes submission:276

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

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Revised: May 25, 2006 1:38 PM .