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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs28364240          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:125/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_021173.2:c.116G>C
NP_066996.2:p.Arg39Pro
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 ss48407383 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28364240 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
ss35037394EGP_SNPS|POLD4-002458byFreqfwd/C/Gctgtcattgcaggggaggagccccagcccccgacgaggaggaagcggagctggagctgct02/25/0511/02/06125Genomicunknown
ss48407383APPLERA_GI|hCV25636040byFreqrev/C/Gagcagctccagctccgcttcctcctcgtcgggggctggggctcctcccctgcaatgacag09/28/0511/03/06126Genomicunknown
ss69319395PERLEGEN|PGP17792411byFreqrev/C/Gagcagctccagctccgcttcctcctcgtcgggggctggggctcctcccctgcaatgacag01/30/0703/31/08127Genomicunknown
ss74890346ILLUMINA|ILMN_Human_1M_rs28364240fwd/C/Gctgtcattgcaggggaggagccccagcccccgacgaggaggaagcggagctggagctgct08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs28364240|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=129
 TGAAGAGGAG GGAGGGGCCC GCTGGGCACA GCAAGGGGGA GCTGGCACCC GAGCTAGGTC
 TCTGAGGTGT GAGGGAGGCA GGAGGAGTGG ACACGGAGGG GCCTAGAGGA GGCCCCTAGA
 GGGGCGGAGG GGCCGATGGA AAGGGAAAGG TGGCCTGTCC TCCCCTCCCG ACACCAGGTC
 TAGCTGCGGG GTGGCAGAGG CAAAGCGGTG GTGAGGAAGG CTGGGAGGTG AGGGGCAGGA
 GACTGAAGCC AACCTCGTAC TGAAGAGCAG CTGTCATTGC AGGGGAGGAG CCCCAGCCCC
 S
 CGACGAGGAG GAAGCGGAGC TGGAGCTGCT GAGGCAGTTT GACCTGGCCT GGCAGTACGG
 GCCCTGCACC GGTGAGAACC CACCCAGCCC CACGGAGGCG CCTCTCCCAG CCAGTCACCC
 ACACGTCTCT GAAGTCACCC AAGCGCTTGC GTGACTCTGA CCCTCAGGAA CTGTCTCCCC
 CCAACACACA CATTCTCCAG CTCAGACTCT ACCCCACCCC CCACAAGTCT CCAGAGTCTT
 CTTCCCACCC TGGCAGGGAT CACACGGCTG CAGCGCTGGT GTCGGGCCAA GCAGATGGGC

  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_000011.8
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss35037394 EGP_YORUB-PANEL Sub-Saharan African 22 IG 1.000 1.000
EGP_HISP-PANEL Hispanic 42 IG 0.048 0.286 0.667 0.752 0.190 0.810
EGP_CEPH-PANEL European 42 IG 0.048 0.952 1.000 0.024 0.976
EGP_AD-PANEL African American 30 IG 1.000 1.000
EGP_ASIAN-PANEL Asian 46 IG 1.000 1.000
ss48407383 AGI_ASP population multiple 72 IG 0.056 0.944 1.000 0.028 0.972
ss69319395 HapMap-CEU European 120 GF 0.033 0.967 0.017 0.983
HapMap-HCB Asian 90 GF 0.022 0.978 0.011 0.989
HapMap-JPT Asian 90 GF 0.044 0.956 0.022 0.978
HapMap-YRI Sub-Saharan African 120 GF 1.000 1.000
Concordant Genotype Total Sample C/C C/G G/G
ss35037394 94 1 6 83
ss48407383 38 34 2
RefSNP Genotype Summary Total Individual C/C C/G G/G
rs28364240 133 35 8 83
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
160 ss35037394 C/G EGP_SNPS EGP_CEPH-PANEL E120 NA12239 POLD4-EGP_CEPH-022405
Genotype data submitted for133 samples from133 individualsIndividual with multiple genotypes submission:0

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

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Revised: May 25, 2006 1:38 PM .