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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs16924241          
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_033439.2:c.789C>G
NP_254274.1:p.Ile263Met
NT_008413.17:g.6246144C>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 ss48426039 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16924241 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
ss23598625PERLEGEN|afd2413972byFreqfwd/TC/Gctcttctgagaatttgtgtactgaaaatatttgtttaagctctctgaaacttagttgatg08/10/0409/13/04123Genomicunknown
ss48426039APPLERA_GI|hCV25964949byFreqrev/C/Gcatcaactaagtttcagagagcttaaacaaatattttcagtacacaaattctcagaagag09/28/0511/03/06126Genomicunknown
ss66437372AFFY|SNP_A-2181709byFreqrev/BC/Gcagagagcttaaacaaatattttcagtacaca10/29/0603/31/08127Genomicunknown
ss69280383PERLEGEN|PGP02413972byFreqfwd/C/Gctcttctgagaatttgtgtactgaaaatatttgtttaagctctctgaaacttagttgatg01/30/0703/31/08127Genomicunknown
ss76215557AFFY|AFFY_6_1M_SNP_A-2181709rev/C/Gcagagagcttaaacaaatattttcagtacaca08/28/0708/30/07130Genomicunknown
ss83105010KRIBB_YJKIM|KHS395733fwd/C/Gctcttctgagaatttgtgtactgaaaatatttgtttaagctctctgaaacttagttgatg11/30/0712/04/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16924241|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 AGCAAGCTTG CTAGAAATAT CAAGTCATAA ATAAGTATTC CCCTTTAGTT TCCAATACAG
 GCAGGTAAAG TTGACTCTGA ACTTCCCATT CACATATGGA TTGCTTTCTC TCTTGTTTCC
 TCAGCTCCAT AAGTGTGAAA AACCACTGCC AGACCAGGCC TTCTTTGTCC TTCATAATAT
 GCACTCCAAC TGTGTTTCAT TTGAATGCAA GACTGATCCT GGAGTGTTTA TAGGTGTAAA
 GGATAATCAT CTTGCTCTGA TTAAAGTAGA CTCTTCTGAG AATTTGTGTA CTGAAAATAT
 S
 TTGTTTAAGC TCTCTGAAAC TTAGTTGATG GAAACCTGTG AGTCTTGGGT TGAGTACCCA
 AATGCTACCA CTGGAGAAGG AATGAGAGAT AAAGAAAGAG ACAGGTGACA TCTAAGGGAA
 ATGAAGAGTG CTTAGCATGT GTGGAATGTT TTCCATATTA TGTATAAAAA TATTTTTTCT
 AATCCTCCAG TTATTCTTTT ATTTCCCTCT GTATAACTGC ATCTTCAATA CAAGTATCAG
 TATATTAAAT AGGGTATTGG TAAAGAAACG GTCAACATTC TAAAGAGATA CAGTCTGACC

  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_000009.9
dbSNP Blast Analysis
UniGene Cluster ID
348390

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 HWP C
 G
ss23598625 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 44 IG 0.864 0.136 0.752 0.932 0.068
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss48426039 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 88 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.900 0.100 0.752 0.950 0.050
AGI_ASP population multiple 68 IG 0.971 0.029 1.000 0.985 0.015
ss66437372 HapMap-CEU European 118 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 0.900 0.100 0.950 0.050
ss69280383 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 0.900 0.100 0.950 0.050
ss76215557 ICMHP 8 IG 1.000 1.000
Concordant Genotype Total Sample C/C C/G
ss23598625 71 67 3
ss48426039 734 27
ss66437372 268 7
ss76215557 6 1
RefSNP Genotype Summary Total Individual C/C C/G
rs16924241 796 68 30
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5259 ss48426039 G/G CSHL-HAPMAP HapMap-YRI NA18857 YOR023.01 r27_ch9_YRI_affymetrix:genomewidesnp_6.0 4014177
5259 ss66437372 G/G CSHL-HAPMAP HapMap-YRI NA18857 YOR023.01 chr9-HapMap-YRI
Genotype data submitted for811 samples from796 individualsIndividual with multiple genotypes submission:275

  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 .