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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs17001989          
refSNP ID: rs17001989
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/129
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_001449.3:c.-26-282A>G
NT_011786.15:g.19499632A>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 ss23833701 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17001989 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
ss23833701PERLEGEN|afd3875692byFreqfwd/TA/Gtccacttgccccgctccgcatcttttgtgatcagcacagttgatatatctgagcaggggc08/10/0409/13/04123Genomicunknown
ss75080058ILLUMINA|ILMN_Human_1M_rs17001989fwd/TA/Gtccacttgccccgctccgcatcttttgtgatcagcacagttgatatatctgagcaggggc08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17001989|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129
 ATAGCACTGC TCAGCCATAC CTCCCAGCAT CCTGTCCCCT ATCTGGTGAC TTGGCCAACA
 CAGGCTCTGA TCCACTTGCC CCGCTCCG
 CATCTTTTGT GA
 R
 TCAGCACAGT TG
 ATATATCTGA GCAGGGGCTT CTACCATCTC CCCAGGGAAT CACTAGCCAT CGGCCATCTG
 GCCCCGCGGG GTGCTTTTGT TCCTGGAA

  GeneView back to top
GeneView via analysis of contig annotation: FHL1 four and a half LIM domains 1
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_011786->NM_001449
function
"
Group
label
Contig-->mRNA-->ProteinContig
position
mRNA
orientation
mRNA
pos
FunctiondbSNP
allele
Protein
residue
Codon
pos
Amino acid
pos
referenceNT_011786->NM_001449->NP_00144019499632forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs17001989 maps exactly once on NCBI human chromosome X
ChromosomeContig
accession
Contig
position
Chromosome
position
Hit
orientation
Contig
Allele
Assembly
Type
Group
label
Contig
label
Neighbor
SNP
SNP_flank
position
XNW_001842404.1322466124560611plusAalt_assembly_8HuRefHuRefview100
XNT_011786.1519499632135115950plusAref_assemblyreferencereferenceview100
XNW_927722.1327150135650934plusAalt_assembly_1CeleraCeleraview100

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000023.5
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL078638.9 AL670274.2

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss23833701AFD_EUR_PANELEuropean 48IG 1.000 1.000
AFD_AFR_PANELAfrican American 46IG 0.870 0.087 0.043 0.050 0.913 0.087
AFD_CHN_PANELAsian 48IG 1.000 1.000
HapMap-CEUEuropean 120IG 1.000 1.000
HapMap-HCBAsian 90IG 1.000 1.000
HapMap-JPTAsian 90IG 1.000 1.000
HapMap-YRISub-Saharan African 116IG 0.931 0.069 0.001 0.931 0.069

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.042+/-0.13933226090

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

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Revised: May 25, 2006 1:38 PM .