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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs6422239          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
XM_001125807.1:c.161C>T
XP_001125807.1:p.Thr54Ile
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 ss118153695 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6422239 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
ss10762134BCM_SSAHASNP|chr15.NT_037852.3_872734fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca06/30/0310/10/03116Genomicunknown
ss11315727SC_JCM|chr15.NT_037852.3_872734fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca07/03/0310/10/03116Genomicunknown
ss12307778WI_SSAHASNP|chr15.NT_037852.3_872734fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca07/04/0310/10/03116Genomicunknown
ss81245229HGSV|Cor18507_SNV_20070510.chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca11/26/0711/28/07130Genomicunknown
ss82251312HGSV|Cor19240_SNV_20070510.chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca11/30/0712/02/07130Genomicunknown
ss84511254HGSV|Cor19129_SNV_20070510.chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca12/06/0712/07/07130Genomicunknown
ss84585218HGSV|Cor18517_SNV_20070510.chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca12/06/0712/07/07130Genomicunknown
ss1138825401000GENOMES|NA19240_2008_12_16_2802577_chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca12/18/0812/18/08130Genomicunknown
ss118153695ILLUMINA-UK|NA18507_000000420_NCBI36.1_chr15_19136466fwd/TA/Gaataagtataaaactcatacctttgcaggttatgtatccagatggctgggttaataaaca01/20/0901/20/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6422239|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 TGTATCACAT CTAAAGATGT TAGAATGCAG TGTTACACAA AGATTCTTTT TTACCTATAG
 TTTCATTTAT TTTACTACTT ATAAATATTT TGATCTCCTG ATACTGCCTA ACACAATTGC
 TGCAGATTAA CTATAAAATA AGCTAAAATG TTCAAATGTT TTCCACTGGA TACTTTAGAT
 CCAGCAACTA TAATGTATAA CATTACACTA AAACAAACTG AATAAGTATA AAACTCATAC
 CTTTGCAGGT
 R
 TATGTATCCA GATGGCTGGG TTAATAAACA AAATATGATC ACAAAGCTGC TTCAGCAAAG
 GTACTCCATG AGATAAACCA TCAAGGTATT TTGCAAAAGA TAAAAATTGC TCCAAGACAG
 GTCTAGTTAT ATGAACTCTT GATGACTAAG AAAGAAAACA GAAATTCTAG CTTGAAATAT
 CCAGAATATT AAATTGTATA ATTTCTGACT TAGCATAAGC ACACATGAAT TTTTCATATG
 CTATCACTAA

  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_037852
dbSNP Blast Analysis

  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
byClusterwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .