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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs769188          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001509.1:c.253C>G
NM_001509.2:c.253C>G
NM_003996.2:c.242-532G>C
NP_001500.1:p.Leu85Val
NT_007592.14:g.19357817C>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 ss35038295 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs769188 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
ss869730UWGC|gpx5-e3+f12fwd/TC/Ggttcctcctctaactgcagaactaaatgcatccaggaggagctgaagccctatggtctag09/12/0110/10/03101Genomicunknown
ss3188790HGBASE|SNP000064525fwd/TC/Gtcctctaactgcagaactaaatgcatccaggaggagctgaagccctatgg07/23/0110/10/0398cDNAunknown
ss35038295EGP_SNPS|GPX5-007745byFreqfwd/C/Ggttcctcctctaactgcagaactaaatgcatccaggaggagctgaagccctatggtctag02/25/0511/02/06125Genomicunknown
ss65842214KRIBB_YJKIM|KHS18008fwd/C/Ggttcctcctctaactgcagaactaaatgcatccaggaggagctgaagccctatggtctag10/17/0611/15/06127Genomicunknown
ss86272619CORNELL|hCV8939974fwd/C/Ggttcctcctctaactgcagaactaaatgcatccaggaggagctgaagccctatggtctag01/21/0801/21/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs769188|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=129
 CTTCAGCTGA TTCTGATGTG CTGCAGGTAT GGAAAACACT GCACCATGAC AAAGGGCTTT
 TGAGCGCACG TCTGAAGATC CGGCCTCTAA CTTCAGCTAT GCTACTAACA GCCCTTCTGA
 TGCAGAGCTG TTTCCCTCCC TGGGCCTCTG TTTCCTTCTC TGTAAAATGG GTAACCCCAG
 GGAATCATCC TTGCACAAGG CAGAACCTCT ACCTAGACCA AAATTGTTCC TCCTCTAACT
 GCAGAACTAA ATGCA
 S
 TCCAGGAGGA GCTGAAGCCC TATGGTCTAG TTGTGTTGGG CTTTCCCTGC AACCAATTTG
 GAAAGCAAGA ACCAGGAGAT AACAAAGAGA TTCTTCCTGG GCTCAAGTAC GTGTCTTCTT
 GAAATCCAAT AGGAGGCGCC TGTGTACCTT TCCTCAGTCT CCAGAGGCCC TTCCAGCTCA
 GGAACTTTCT GGGGAGGTAT GGATTAATAG GCTCAGGGGC ATTACAAGCA GAGTTTAACT
 TTGGCCTACC GTGAT

  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
NM_001509,AL
dbSNP Blast Analysis
UniGene Cluster ID
248129

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 HWP C
 G
ss35038295 HapMap-CEU European 120 IG 1.000 1.000
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
EGP_YORUB-PANEL Sub-Saharan African 16 IG 0.875 0.125 1.000 0.938 0.062
EGP_HISP-PANEL Hispanic 34 IG 0.941 0.059 1.000 0.971 0.029
EGP_CEPH-PANEL European 34 IG 1.000 1.000
EGP_AD-PANEL African American 20 IG 0.900 0.100 1.000 0.950 0.050
EGP_ASIAN-PANEL Asian 38 IG 1.000 1.000
ss65842214 KHP1 180 AF 1.000 1.000
ss869730 NIHPDR Global 74 IG 0.973 0.027 1.000 0.986 0.014
CEPH 184 AF 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.010+/-0.069 599 483 58 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 YES

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Revised: May 25, 2006 1:38 PM .