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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11549789          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_023078.2:c.206G>A
NP_075566.2:p.Arg69Gln
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 ss48426411 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11549789 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
ss16249694CGAP-GAI|1498450fwd/TA/Gacctatgtcactttcaagctctgggttgccgaccacgcactccaaccaggaggtgctgca11/18/0311/22/03120cDNAunknown
ss48426411APPLERA_GI|hCV25613748byFreqfwd/TA/Gtggtgtccctggcgcaggctctgggttgccgaccacgcactccaaccaggaggtgctgca09/28/0511/03/06126Genomicunknown
ss69066361PERLEGEN|PGP17792007byFreqrev/BC/Ttgcagcacctcctggttggagtgcgtggtcggcaacccagagcctgcgccagggacacca01/30/0703/31/08127Genomicunknown
ss74898080ILLUMINA|ILMN_Human_1M_rs11549789fwd/TA/Gtggtgtccctggcgcaggctctgggttgccgaccacgcactccaaccaggaggtgctgca08/28/0708/29/07129Genomicunknown
ss84493765HGSV|Cor19129_SNV_20070510.chr8_144760432rev/BC/Ttgcagcacctcctggttggagtgcgtggtcggcaacccagagcctgcgccagggacacca12/06/0712/07/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11549789|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GCGTGCATGT GCATGGGTGT GTTTGCATGC TGGGTGGTGG TCACAGACAT TCACTGGGGA
 TGGAGGGCTC AGGGCTTGGG GAGGCGCTGA CATCAGGATG GCCTGTGAGG AGTAGGGCTA
 GTCTGCGGGA GTCTTGGGCA CTGGAGAAGT CGGGGTGGTC TAGACACTTG CAATGGGAGA
 GGCCCTGGGA CCATGGGAAC GTGTGGCATC CAGCAGGAAG GGCTGTGATG GAGAGGGTGC
 GCCGCTTACA TGGCCCCTGA GGCTTGGTCC TGGTGTCCCT GGCGCAGGCT CTGGGTTGCC
 R
 GACCACGCAC TCCAACCAGG AGGTGCTGCA GAGCTGCCTG CTCGTCATCT TTGCCACCAA
 GCCTCATGTG CTGCCAGCTG TCCTGGCAGA GGTGGCTCCT GTGGTCACCA CTGAACACAT
 CTTGGTGTCC GTGGCTGCTG GGGTGTCTCT GAGCACCCTG GAGGAGGTGA GTGTCCCTTG
 GGCTAAGGCC TTGGTCCCAG TATAGGCTCT GCTGGCCAGG CTTGGGCGGC AGGCAGCCCC
 CCAGAGAGCC TGAGAGGTGG CCGTGTGGCC CACCTGGATC AAGTGGCTGG ATTTAGGGTT

  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_000008.9 BM548059
dbSNP Blast Analysis
UniGene Cluster ID
165186

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss48426411 AGI_ASP population multiple 74 IG 0.189 0.811 0.527 0.095 0.905
ss69066361 HapMap-CEU European 120 GF 0.067 0.933 0.033 0.967
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 0.017 0.200 0.783 0.117 0.883

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.096+/-0.197 1119 914 225 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 UNKNOWN

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Revised: May 25, 2006 1:38 PM .