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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs4989413          
refSNP ID: rs4989413
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:113/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_000663.3:c.816+1265T>C
NM_020686.4:c.816+1265T>C
NT_010393.15:g.177174T>C
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 ss84741729 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4989413 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
ss7847405DEVINE_LAB|DB_1_19338fwd/BC/Tgctcactgcaagctccgcctcctgggttcagccattttcctgcctcagcttcctgagtag03/16/0310/10/03113Genomic96 %
ss40734082ABI|hCV26739008fwd/BC/Tgctcactgcaagctccgcctcctgggttcagccattttcctgcctcagcttcctgagtag07/17/0507/17/05126Genomicunknown
ss84741729HGSV|Cor19129_SNV_20070510.chr16_8771596fwd/BC/Tgctcactgcaagctccgcctcctgggttcagccattttcctgcctcagcttcctgagtag12/06/0712/07/07130Genomicunknown
ss90313129BCMHGSC_JDW|JWB-0918149fwd/BC/Tgctcactgcaagctccgcctcctgggttcagccattttcctgcctcagcttcctgagtag02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4989413|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CCTACCCCCC GTTTCCACGT CATCTAACAC AGCCCTCTTT AGATCCACTC AGTATATGGG
 GGTTCCAGGG AAGACATTGG AAGTAATCTG CAGCTGGAAA AAAATATCAC TGTTTGGGTA
 TAGATTTGAA CTCAAATAAG GCTGCTGGTT TTTTTCTTAG GCACATCATC ATTTTCAATC
 AGTTCATATT TATTGAGCAC CTACTAGATG TCAAGCAAGG TGCTAGGTGC TGGGTATTCA
 GTGGTAAATA GAAAAGACAA GATAATGGCA TCAAGTACAG CACTGTCCAA TAGAAATATA
 ATGCAAGCCA CATATGTAAT TATAGCTTTT CCAGTAGTCA CCTTTTCTTT CATTTTTACA
 CCCTGCCTGG AAACTGCCAA GGAGTCACAT TTGCTTTGTT TTGTTTTGCT TTGTTTTTGA
 GATGGAGTCT AGCTCTGTTG CCCAGGCTGG AGTGCAGTGG CGCGATCTCA GCTCACTGCA
 AGCTCCGCCT CCTGGGTTCA
 Y
 GCCATTTTCC TGCCTCAGCT TCCTGAGTAG CTGGGACTAC AGGCGCTTGA CACCACACCC
 GGCTAATTTT TTGTATTTTT AATAGAGACA GGGTTTCACC GTGTTAGCCA GGATGGTCTC
 GATCTCCTGA CCTTGTGATC CGCCCGCCTC GGCCTCCCAA AGTGCTGGGA TTACAGGTGT
 GAGCCACCGC GCCGGCCTTC TTTTCTTTTG TTTTGTTTGA GACAGGGTCT CACTCTGTCA
 CCCAGGCTGG AGTGCAGTGG TGCAATCACA GCTCACTGCA GTCTCGACCT CTCTGGGCTC
 AGGTGATCCT CCCACCTCAG CTTCTTGAGT AGTTGGAACT AAGGCACATG ACACCACCAC
 ACCTGGCTAA TTTTTGTATT TTTTGCAGAA ACAGGTTTTG CCGTGTTGCC CAGGTTGGTC
 TCAAACTCCT GGGCCCAAGT GGTCTGCCCA CTTCGGCTTC CCAAATTGCT GGGATTACAG
 GTGTGAGCCA CCGTGCGTGG

  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
function
referenceNT_010393->NM_020686
function
HuRefNW_001838342->NM_000663
function
HuRefNW_001838342->NM_020686
function
CeleraNW_926018->NM_000663
function
CeleraNW_926018->NM_020686
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010393->NM_000663->NP_000654177174forwardintron
referenceNT_010393->NM_020686->NP_065737177174forwardintron
HuRefNW_001838342->NM_000663->NP_000654177831forwardintron
HuRefNW_001838342->NM_020686->NP_065737177831forwardintron
CeleraNW_926018->NM_000663->NP_0006548749135forwardintron
CeleraNW_926018->NM_020686->NP_0657378749135forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs4989413 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_010393.151771748771596plusTref_assemblyreferencereferenceview400
16NW_001838342.11778318786556plusTalt_assembly_8HuRefHuRefview400
16NW_926018.187491359033485plusTalt_assembly_1CeleraCeleraview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010530
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
with2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .