NCBI

NLM

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
Spacer gif
BUILD 129
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs3954997          
refSNP ID: rs3954997
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:108/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001170.1:c.27-2839G>A
NT_008413.17:g.33388032C>T
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 ss5244750 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3954997 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
ss5244750TSC-CSHL|TSC1764830fwd/BC/Tttgagcaattactatgcagtgtgatgagcatgccccagctgaaagagtgggcaccgtggg09/20/0210/10/03108Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3954997|allelePos=500|totalLen=995|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=108
 NNNNNNNATA CAGCCAGAGG GTGGGCAGGG GTGAGCCTAT CAACAGAGGT GTCTCAGTTG
 AAATAGTGGA AGATGTTTGA TTCCATGCTG GGACATCTCT CATTCCCTCT GCTTACTTTT
 TGCTGCTGTG AGGTCAGGGG AATTTAGGAG CCCTGAGGAA TGCTGCTGCT CTCCCTAGCA
 GGGCGAGGTG ACCCTCCACT GGCCCCCATC CAACCCCAGC TCCCATGCTG GAGGTAACCA
 CAGAAGAGGA GAGAGAAGTG GATAGAGCAG AAAGCCAAGA ACACCAAGAG AATCCTGGAA
 GCCTGGCTCC TTCCTCATCA CCACACAGCT GGCAAGACAC AGTAAGCAAC AGATAACCAC
 CAACCAGCCA ATGAACTCAA GATTTCTTGA ATCTACTGTG CCTAGAATGT TCAGACACTG
 CAGTAAAGGA CACTGGTACG ATCCAGCCCG TGGGAAGAAA AGCAATCAAT TGAGCAATTA
 CTATGCAGTG TGATGAGCA
 Y
 TGCCCCAGCT GAAAGAGTGG GCACCGTGGG GCATGTGGAG GAAGTGAATG GCCTAGAGGA
 GGGGGTAGGA GGCTCCCAGA GAAAGGGAAA TTTAGGTCAA GAAAAGAAGG CTGGAGGGTA
 AAGGAGCCTC CAGGGAGGCA GGGATCACTC TGGGCGTAGG ACTGGCATGT GCAAAGGCCT
 GCAGCTAAGG CAGTATCCAA TGTGCAGGAA TGGGCTGGCC ACGGAGGAGT GGAGGTGGCA
 TGAGATGGGC AGAGAGGGGC CAGGGCCAGG TGGCAGAAGG CCTCATGGCC CACATTAGGG
 AGTCTGAACT CTACCAGAGG GCCATGGGCC AAGTGGAGGG TTTCAGCAGG AGAGCTGCCT
 CCCCTGTGGA GGCCAGGATG GAGGAAGTGG AGTGGAGGCA GGGTGAGCAT CAGCTTCTCC
 ACAGATGGGT GGAGAAGTGG CGGCAGCCTG AGCCACAGAG ATGGCAGCGC CAATGGCCAA
 AAGAGCACAG TCAAG

  GeneView back to top
GeneView via analysis of contig annotation: LOC730908 similar to Aquaporin-7 (AQP-7) (Aquaporin-7-like) (Aquaporin adipose) (AQPap)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
GeneView via analysis of contig annotation: AQP7 aquaporin 7
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
HuRefNW_001838807->XM_001717938
function
HuRefNW_001838807->XM_001717941
function
referenceNT_008413->NM_001170
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
HuRefNW_001838807->XM_001717938->XP_001717990855335reverseintron
HuRefNW_001838807->XM_001717941->XP_001717993855335reverseintron
referenceNT_008413->NM_001170->NP_00116133388032reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs3954997 maps exactly once on NCBI human chromosome 9
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NW_001838807.285533589287211plusTalt_assembly_8HuRefHuRefview499
9NW_924062.13321267133328152plusCalt_assembly_1CeleraCeleraview499
9NT_008413.173338803233388032plusCref_assemblyreferencereferenceview499

  NCBI Resource Links back to top
Submitter-Referenced
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL356218.22 AL353675.13

  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

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .