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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs16866827          
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_138799.2:c.*675A>G
NM_138799.2:c.1501A>G
NP_620154.2:p.Thr501Ala
NT_005334.15:g.3833006T>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 ss48421041 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16866827 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
ss23207468PERLEGEN|afd1224070byFreqfwd/BC/Ttttcttgattctgattgcaaacattgtttgtgtagaaaaactgttctgtcccaaagaatt08/10/0409/13/04123Genomicunknown
ss48421041APPLERA_GI|hCV25962240byFreqrev/TA/Gaattctttgggacagaacagtttttctacacaaacaatgtttgcaatcagaatcaagaaa09/28/0511/03/06126Genomicunknown
ss68803335PERLEGEN|PGP01224070byFreqfwd/BC/Ttttcttgattctgattgcaaacattgtttgtgtagaaaaactgttctgtcccaaagaatt01/30/0703/31/08127Genomicunknown
ss74882299ILLUMINA|ILMN_Human_1M_rs16866827fwd/BC/Ttttcttgattctgattgcaaacattgtttgtgtagaaaaactgttctgtcccaaagaatt08/28/0708/29/07129Genomicunknown
ss91049559BCMHGSC_JDW|JWB-1198057fwd/BC/Ttttcttgattctgattgcaaacattgtttgtgtagaaaaactgttctgtcccaaagaatt02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16866827|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 TGGGAGTGCC CACTGAAATA TGGAAATATT CTTACATAAG GCGTGGCCCA CGGGGACATG
 GCATGGGAGG GCTTGTTTCA CTCCATTTCC AATCTGGTGT ACAGGAAATT CCTTATCTAT
 AACTGTCCAT TTCCCCCCAG TTAACTGCTT TTCCAACAAA CTCAAACCCC TTGAAAAGGT
 GCTAAGATTG GTTTCTGTTA ACATCAAAAA AAAAAAACAG CCCTCAGAGC CTTCCCGATC
 ACTGCTTTAG TGATGAATGT CTCGAGGCTA TTTCTTGATT CTGATTGCAA ACATTGTTTG
 Y
 TGTAGAAAAA CTGTTCTGTC CCAAAGAATT TTCTCCTTCA TCAAACTTTT TGGATTGTGA
 GAGCTGAATG TTTTCATGTG TATTCTTTCT TCTTTGAGTT TTTTTCACTG GCAACAACAA
 TAATACTAAG ATACCAAGAA TGTGCAGGCA ATAATACCAG GAGCTAAAAG AAAAAGGGAA
 AAAGTTTATT AAAACTTGAT AATTAATAAT CCTTAATAAC TGCACACTTG TCAAAATGTC
 ACATGGCCCA CCTTAGGATG TATTTGTTTA CTACATTACT ACATTATTCT TTTATTTTTC

  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_000002.9
dbSNP Blast Analysis
UniGene Cluster ID
467634

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss23207468 AFD_EUR_PANEL European 48 IG 0.042 0.958 1.000 0.021 0.979
AFD_AFR_PANEL African American 46 IG 0.043 0.957 1.000 0.022 0.978
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss48421041 HapMap-CEU European 120 IG 0.017 0.100 0.883 0.150 0.067 0.933
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 1.000 1.000
AGI_ASP population multiple 68 IG 0.059 0.941 1.000 0.029 0.971
ss68803335 HapMap-CEU European 120 GF 0.017 0.100 0.883 0.067 0.933
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

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.037+/-0.132 951 768 276 0

  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 .