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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs9890088          
refSNP ID: rs9890088
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001488.3:c.192+1703G>A
NM_133439.2:c.192+1703G>A
NT_078100.1:g.1062963G>A
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 ss13727469 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9890088 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
ss13727469BCM_SSAHASNP|chr17.NT_078100.1_1062963fwd/TA/Gagctatcctatctcagccacctgactagctggactataggcacaagccaccatgcctggc11/05/0311/22/03119Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs9890088|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=119
 acagttctgt ggatcagaag atcattaggc tcagctggtt tgctccaggt tccataaggc
 tgaaatgaag atgttggcca gcctgggctc tcacctggag gccctggggt agaatccact
 tctaggttct ttcaggttgt tggcagaatt cactgcctta aggttttagg aaggatgcca
 ctgttttgat cagggcatgt tctccgtttc cacaggctgt ctgcattccc tggctctggg
 ccccctttct ccatcctcaa agccaggagc acaggaagtc cttgaggttg ttgatgaaat
 ccagggaatc tctatgacct ctcctattgc cttatctttc CTGTGCTGAA TCTTTATGAG
 TGATTCTTCT GCTTTCCTCT TCTACtttga gacagggtct cactctatca cccaggctaa
 agagcagtgg cacaatcaca gctcactgta acctcgacct cccaggctta agctatccta
 tctcagccac ctgactagct
 R
 ggactatagg cacaagccac catgcctggc taatttAAAA ATTTTTTTTG TAggccaggc
 ttggtggctc atgcctgtaa tcccagcact ttgggaggcc gaggcgggtg gatcacaagg
 tcaggagatc gagaccatcc tggctaacat ggtgaaaccc catctctact aaaaacacaa
 aaaattagcc aggtgtggtg gtgggcgcct gtagtcccag ctactcggga ggttgaggcg
 ggagaatgat gtgaacccgg gaggcagagc ttgtattgag ccaagattgt gccactgcac
 tccagcctgg gcaacagagt gagactccgt ctcaaaaaaa aaaaaaaaag aaaaagaaaa
 aTTTTGTAGA CAGGGGTCTA GGGGCCTTTC TATGTTATTC AGGCGTCTAg gggtctttct
 gtgttattca ggctggtctc aaactcctgg gctcaagtga tcctcccacc tcaaccctca
 acctcctaaa gtgctgggat

  GeneView back to top
GeneView via analysis of contig annotation: TADA2L transcriptional adaptor 2 (ADA2 homolog, yeast)-like
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_078100->NM_001488
svfunction
referenceNT_078100->NM_133439
svfunction
HuRefNW_001838434->NM_001488
svfunction
HuRefNW_001838434->NM_133439
svfunction
CeleraNW_926817->NM_001488
svfunction
CeleraNW_926817->NM_133439
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_078100->NM_001488->NP_0014791062963forwardintron
referenceNT_078100->NM_133439->NP_5976831062963forwardintron
HuRefNW_001838434->NM_001488->NP_001479475943reverseintron
HuRefNW_001838434->NM_133439->NP_597683475943reverseintron
CeleraNW_926817->NM_001488->NP_001479979775forwardintron
CeleraNW_926817->NM_133439->NP_597683979775forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs9890088 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_001838434.247594331726609minusCalt_assembly_8HuRefHuRefview500
17NW_926817.197977532611806plusGalt_assembly_1CeleraCeleraview500
17NT_078100.1106296332862924plusGref_assemblyreferencereferenceview500

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_078100
dbSNP Blast Analysis
GenBank HTGS Finished:
AC004099.1 NC_000017.9

  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
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .