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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs12598010          
refSNP ID: rs12598010
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_000663.3:c.1269+720T>C
NM_020686.4:c.1269+720T>C
NT_010393.15:g.184146T>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 ss20022110 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12598010 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
ss20022110CSHL-HAPMAP|CSHL-HuFF-200402.chr16.NT_010393.14_184146fwd/BC/Tagcatgggccaccgtgcccggccctggttacttttgacaccaatttcagacatcccccct02/21/0403/04/04120Genomicunknown
ss83979313HGSV|Cor18555_SNV_20070510.chr16_8778568fwd/BC/Tagcatgggccaccgtgcccggccctggttacttttgacaccaatttcagacatcccccct11/27/0712/06/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12598010|allelePos=501|totalLen=919|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGGTTTTCT TTGTTGTTGt tttttttaat ttatttttta tttttttaat attgagacat
 ggtcaagctc tgttagccag tccggccttg aactcctggc ctcaaacgat ccttccacct
 cagcctccca aagtgctggg CAGCGCCTGC CGGCACTGGT TATCTTTCTT Atttatttta
 ttttatttta tttGTCTAtt tattttttga gaccaagtct tgctttgtac ccaggctgga
 gtgcagtggc gcaatctcag ctcaccgcaa ccgctgcctc ctgggttcag gagattctcc
 ggcctcagcc tcccaagtag ctgggattac gggcatgtgc cgttatgccc tactaatttt
 tttgtatttt gaatagagac agggtttcac catgttggcc aggctggtct cgaacccccg
 acctcaggtg atccgcttgc ctcagcctcc caaagtgctg ggatttcacg agcatgggcc
 accgtgcccg gccCTGGTTA
 Y
 CTTTTGACAC CAATTTCAGA CATCCCCCCT TTGAGAGTCC CCCAAGCACT CCCTCTCTCA
 CCCCCTCTAG TGTGTTCATT ATTCCCGCCT TTGTGCAACC TGTTGCATAC TTACCACTCG
 GCAGCACTGC CCTCCCCTGC TGGAGCTGGA ttactctcta ccctcaaggt ttcgtcatgg
 gccaaaatgg ctcctggagc tccagccatc gcatctcaat tccaggcaat aggaaggaaa
 aagaagggaa ggacagagtg gcccccttct tgtctttagc agccttccca gaaatctcac
 ataatacttc taacacttga ttaagagctg gtcacgtggt cactcctaac cgtaaggacg
 tgtggggaTG TGTGTGTGTG AGTGTGGCAG GCAGGCCTAA AGGGGTGTCT AAATGGAA

  GeneView back to top
GeneView via analysis of contig annotation: ABAT 4-aminobutyrate aminotransferase
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_010393->NM_000663
svfunction
referenceNT_010393->NM_020686
svfunction
HuRefNW_001838342->NM_000663
svfunction
HuRefNW_001838342->NM_020686
svfunction
CeleraNW_926018->NM_000663
svfunction
CeleraNW_926018->NM_020686
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010393->NM_000663->NP_000654184146forwardintron
referenceNT_010393->NM_020686->NP_065737184146forwardintron
HuRefNW_001838342->NM_000663->NP_000654184808forwardintron
HuRefNW_001838342->NM_020686->NP_065737184808forwardintron
CeleraNW_926018->NM_000663->NP_0006548756095forwardintron
CeleraNW_926018->NM_020686->NP_0657378756095forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs12598010 maps exactly once on NCBI human chromosome 16
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
16NT_010393.151841468778568plusTref_assemblyreferencereferenceview500
16NW_001838342.11848088793533plusTalt_assembly_8HuRefHuRefview500
16NW_926018.187560959040445plusTalt_assembly_1CeleraCeleraview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010393
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/T
T/T
HWPC
T
ss20022110HapMap-CEUEuropean 118IG 1.000 1.000
HapMap-HCBAsian 88IG 0.023 0.977 1.000 0.011 0.989
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 116IG 1.000 1.000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.005+/-0.04927021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
withHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .