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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs231489          
refSNP ID: rs231489
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_005374.3:c.31+1498A>G
NT_010783.14:g.634105T>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 ss1825093 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs231489 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
ss299310KWOK|OVLP-000621-310949fwd/TA/Ggacagcagtgagccctcatcgtagacatatcatccatgcacaaaaggtatattctactct06/30/0010/10/0379Genomic97 %
ss489567SC_JCM|AC015937.3_130816rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc07/12/0010/10/0387Genomicunknown
ss1224351KWOK|OVLP-000804-272477fwd/TA/Ggacagcagtgagccctcatcgtagacatatcatccatgcacaaaaggtatattctactct09/02/0010/10/0386Genomic97 %
ss1825093KWOK|OVLP-000925-233566fwd/TA/Ggacagcagtgagccctcatcgtagacatatcatccatgcacaaaaggtatattctactct10/05/0010/10/0387Genomic97 %
ss3159305TSC-CSHL|TSC1278254fwd/TA/Ggacagcagtgagccctcatcgtagacatatcatccatgcacaaaaggtatattctactct06/08/0110/10/0396Genomicunknown
ss5589806BGI|pd15_5083.z1.abd_88fwd/TA/Ggacagcagtgagccctcatcgtagacatatcatccatgcacaaaaggtatattctactct10/17/0210/10/03110Genomicunknown
ss6252389SC_JCM|NT_010755.10_738271rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc01/10/0310/10/03111Genomicunknown
ss16152822SC_SNP|NT_010783.14_634105rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc11/18/0311/22/03120Genomicunknown
ss19365191CSHL-HAPMAP|CSHL-HuDD-200402.chr17.NT_010783.14_634105rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc02/20/0403/04/04120Genomicunknown
ss43975489ABI|hCV2814422byFreqrev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc07/18/0511/03/06126Genomicunknown
ss78425931HGSV|Cor12878_SNV_20070510.chr17_39335826rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc10/17/0710/19/07129Genomicunknown
ss79043289HGSV|Cor18507_SNV_20070510.chr17_39335826rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc10/19/0710/21/07129Genomicunknown
ss83315749HGSV|Cor18555_SNV_20070510.chr17_39335826rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc11/27/0712/04/07130Genomicunknown
ss85684417HGSV|Cor18517_SNV_20070510.chr17_39335826rev/BC/Tagagtagaatataccttttgtgcatggatgatatgtctacgatgagggctcactgctgtc12/06/0712/10/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs231489|allelePos=1015|totalLen=1215|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 GAAGGAACAA GAATACCAGG TTAGGATACC TGGACGTGGC TCTGTAGGAG GCATTAGGAC
 AAGGGAGTGG GCCACTCAGA CAAACTAGCA AAGCCTCAGT GGCAAACTGC TTAACCTCTT
 GGAGCTCGCA TTTCTTCTTC TGTAAAGAGG CTGCTGTGAG ACGCAAAGGC TGTAATGGGA
 GAGCACATTA CTTTTAGGAA TAGTCATAAT TATTATGCTG CTGTTGCTGC CGCTGCCACC
 AAGTTGTTGT TGTTGttttt gagacaagtt ctggctcttt agcctaggct ggagtgcagt
 ggcgcaagct tggctcactg caacctctgc ctaccagcct caagtcattc tcccacctca
 gcctcccaag tagctgggac tacaggtgtg caccaccatg cccagctaat ttttgtattt
 ttcgtaaaga caaaaatgtt gcccatgctg gtctcaaact cctgagctca agtactccac
 ccgcctcgac ctcccaaact actgggatta caggtgtgaa ccactgtgcc tggccTGAGT
 TGTTATTTTG GCATTAACCC TGTGTCCTTG AAACAGTCAC CTCCTTTTGA AGACCTGAGA
 TTTCCCTAAG ATGAGATGAT GGGACAAGAT CAGTGTTCTT AACttttttc tttttctttt
 tttttttttt tgagatggag tctccctctg ttgcccaggc tggagggcag tggtgggatc
 tcggctcact gcaaccttca cctcccaggt tcaagtgatt ctcctgcctc agcctcccaa
 gtagctggga ttacaggcac ctgctatcat gcccagctaa tttttgtatt tttgtagaga
 ctgggtttca ccatgttggc caggctgtcc tgacctcagg tgatccacct gccttggcct
 cccaaagtgc tgggattaca ggcatgagcc accacacctg gccTGTTCTT AATTTTATTG
 GTCCTGAGTC ACTTAGAATC TGGTGACAGC AGTGAGCCCT CATCGTAGAC ATAT
 R
 CATCCATGCA CAAAAGGTAT ATTCTACTCT AGGGGATCAT GGATTCCCGT AGTGCACGCA
 GGACCCCAGA AGGTTAAGTT CCCTGTGCTA GAGGCCCTCT GAGGCCCGGG CAGCTGGGAA
 CTGCTATGGT TCTGCTCTGA GTTGTCTGAA CTTCCCCCTG CCTGGATGCC TCCCTCCCAT
 GCAGCTCCTT CCCTTGCTCT

  GeneView back to top
GeneView via analysis of contig annotation: MPP2 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_010783->NM_005374
svfunction
HuRefNW_001838437->NM_005374
svfunction
CeleraNW_926839->NM_005374
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010783->NM_005374->NP_005365634105reverseintron
HuRefNW_001838437->NM_005374->NP_0053651553726forwardintron
CeleraNW_926839->NM_005374->NP_005365575378reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs231489 maps exactly once on NCBI human chromosome 17
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
17NW_001838437.2155372637744601plusAalt_assembly_8HuRefHuRefview1014
17NW_926839.157537838688337minusTalt_assembly_1CeleraCeleraview1014
17NT_010783.1463410539335826minusTref_assemblyreferencereferenceview1014

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010783 AC007993 AC015937.3
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC007993.15 NC_000017.9 AC078837.3

  Population Diversity back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceHWPA
G
ss43975489AoD_African_American 90AF 0.560 0.440
AoD_Caucasian 92AF 0.630 0.370
AoD_Chinese 90AF 0.320 0.680
AoD_Japanese 90AF 0.360 0.640

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.498+/-0.0320000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hit
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .