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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11542387          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
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_003636.2:c.255T>C
NM_172130.1:c.213T>C
NT_021937.18:g.679675T>C
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 ss52069073 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11542387 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
ss16231815CGAP-GAI|1471756fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaaggct11/18/0311/22/03120cDNAunknown
ss43941349ABI|hCV1255663fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac07/18/0507/18/05126Genomicunknown
ss52069073SI_EXO|NT_021937.17_679675fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac03/29/0603/29/06127Genomicunknown
ss86238381CORNELL|hCV1255663fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac01/21/0801/21/08129Genomicunknown
ss99183402HUMANGENOME_JCVI|1103675012087fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac04/03/0804/03/08130Genomicunknown
ss1079656221000GENOMES|CEU.trio.12.15.2008_7614_chr1_6064895fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac12/15/0812/15/08130Genomicunknown
ss118470721ILLUMINA-UK|NA18507_000007505_NCBI36.1_chr1_6064895fwd/BC/Tggcctatgataatggcatcaacctcttcgaacagcagaagtctacgcagccggcaagtac01/21/0901/21/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11542387|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTAAGTAGAC ATGAATTCTG TGGGGATACT GTTCGACCCA GTACAGGTGC TAAGCCCTGT
 GATGACCCCA ACTGATGGGG TCCCTGCTCT CAAGAAATTC ACAGTCCTTG GCAGTTTCTT
 CATTCCTTTT GCCTTCTTTA TTCTTCTCAA TGGGTTTGTT ACTGAGAGCT GCCTCCATCC
 CTGTCCTGTG GCAGGAGAGG GCAAGGAGAC AGCCCACAGG GGAGCCTGTC GGGCCCGGGA
 GGGCAGGGCC TGGACACGGG GAGGCCTCCC AGGCCGAGAG GGTGGTGCTC CAGAGCCTCT
 GGGCCCCACC CCCGGCTGGC AGGACAGTGT CGGTTTTCTC GTTTCAGATG GCAGAGCAGC
 TCATGACCTT GGCCTATGAT AATGGCATCA ACCTCTTCGA
 Y
 ACAGCAGAAG TCTACGCAGC CGGCAAGTAC GTGTCTTTTC ACACGGGAAA AAGTGGTTCA
 GAATGCCTGG GCAGAGCCGG AGCTACAGGG ATTCCTGCCG CTCGCGTTCC CAAGAGTGCT
 CACAAATGCA CCTTGCACCC TGCTTTCATT TTTAAACTCT GAATGGCTTT AGGAGGTGCT
 ATTTTCATGG GGCTGGAATT GCAGAACACT TGGACACTGA TCACTTGCTG AACTCCCCGT
 GGAGCCACCA GGGGGACCAC AGTCCCTCTG GTGCCAAAGA TGCTGTGCTG GGTGAGAGGC
 GCGATGGAGC TGCTGTCCTG GGCTCTCCTG ATGTGCCTGA CATTTTGACA TTTCATGTCT
 CACTTGTGCA ACTAGGGCTG CAGGGCCTCA GAGCTGGGGA

  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
NT_021937.17 ABBA01035435 BQ073672
dbSNP Blast Analysis
UniGene Cluster ID
440497
3D structure mapping
NP_003627  NP_742128  

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterwithHapMapFreqWith1000GenomeData UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .