Skip to main content
NCBI
 dbSNP
PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
transparent GIF
Spacer gif
BUILD 130
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs887540          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
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_000666.1:c.536A>G
NP_000657.1:p.Asn179Ser
NT_022517.17:g.51960670A>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 ss1315654 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs887540 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
ss1315654TSC-CSHL|TSC0155918fwd/BC/Tctataaaagacagtgaaggcatcagtgggatggctatgcctgaggagggaaagggggttc09/06/0010/10/0386Genomic95 %
ss5461707TSC-CSHL|TSC0184790rev/TA/Ggaaccccctttccctcctcaggcatagccatcccactgatgccttcactgtcttttatag09/21/0210/10/03108Genomicunknown
ss74911344ILLUMINA|ILMN_Human_1M_rs887540fwd/BC/Tctataaaagacagtgaaggcatcagtgggatggctatgcctgaggagggaaagggggttc08/28/0708/29/07129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs887540|allelePos=231|totalLen=524|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 GTTTCTGCCC ATTCAGGGCT TGCCCTCAGA GAAGCTCAGA TAGGAAAGAG CTGGGAGGTA
 GAGGCCCTGG GTTCAAGGCC TTCTCAGGCC TCAACTTTGC TGTGCAACCC TGCATAGGAC
 CGTGCCCTTT CTGGCCTAGC CTCCCGCCTG TAGAGTGAGC CCTCCCTCCA AGCTCATACT
 TACACCAGGG ACTCCGCTCA CTATAAAAGA CAGTGAAGGC ATCAGTGGGA
 Y
 TGGCTATGCC TGAGGAGGGA AAGGGGGTTC AGAGGGTGGA GCAGCTCAGT CCCCACTAGC
 AGCCTCCTAC TCCCTGCCTG GCTGCTCATT GGCTTGCCAA CCTGCTCACC CTCATCCAGG
 GCAAAGCCTG CCCTCAGGGC GTGGAACTCA GGCCGCTGCA CGAACAGCTC CATGCCTTGG
 TGACCCCCAA CCTCCTCATC TGTAAAAGCA GCAGGGACGT GAGATGAGGA GGCTGCCCCG
 CCCCACCCTC CCCTTTCCCA AAGGTATCTG AGCCACTCCT ACCAGGCACA AAG

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
AC006255.9 AC027396.3
dbSNP Blast Analysis
UniGene Cluster ID
334707

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/T
 T/T
 HWP C
 T
ss1315654 CEPH 184 AF 1.000
HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 88 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.017 0.983 1.000 0.008 0.992

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.005+/-0.049 869 691 0 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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 .