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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs6602939          
refSNP ID: rs6602939
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/129
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
NT_077631.1:g.208430C>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 ss10795846 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6602939 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
ss10795846BCM_SSAHASNP|chr15.NT_077631.1_208430fwd/BC/Taatctaatgagacctttgtcatgtatgtggctgttgttcacccaaatatcaaaatgtgca06/30/0310/10/03116Genomicunknown
ss12338399WI_SSAHASNP|chr15.NT_077631.1_208430fwd/BC/Taatctaatgagacctttgtcatgtatgtggctgttgttcacccaaatatcaaaatgtgca07/04/0310/10/03116Genomicunknown
ss19319585CSHL-HAPMAP|CSHL-HuDD-200402.chr15.NT_077631.1_208430fwd/BC/Taatctaatgagacctttgtcatgtatgtggctgttgttcacccaaatatcaaaatgtgca02/20/0403/04/04120Genomicunknown
ss90087384BCMHGSC_JDW|JWB-0828260fwd/BC/Taatctaatgagacctttgtcatgtatgtggctgttgttcacccaaatatcaaaatgtgca02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6602939|allelePos=1133|totalLen=1521|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=129
 TTTTTATGAA CCACATGCAT AACAAAACTT TGTCCAATTC CTCCACTTTA TCAGAGACTG
 CCTGCAGGAT GAATTTCAAT GCCATCTAAT TTAGAGTAGG AGCAAAACTT AAAATCCTCT
 ATAGGTCTGA GTGCCACTaa caaccaaaaa aaatttcgac cattatgaag ttttaagaga
 tgccacaatg acagcctggg ttgataggtg atggcatttt ccctgagcat attctgtgaa
 gagtgattat ggtagctttt ccttctaatg aggagaaagc aacagagaaa gtaaaaaaaa
 taataataat aatcacgaaa cagaaaaaag tggcccaaat tgtttaacaa aaaaaaagca
 ctagaaactg ccacaaatta aaaggagata tattgattac ctagcagaaa attcaaagta
 aaccttataa atatgttcac tgagctaggg gaagaatgca cgaacaacat gaaagtatta
 acagggaCAA AAAAGGGAGA GAGATGAGAT ACAATGATTT GTGGCTTAAC AGTAGGGATA
 CATTggccag gcgcagtggc tcatgcttgt aatcccagca ctttgggagg ccaaagagtg
 tggatcacct aggtcacgag ttcaagacca gccagggcaa catggtgaaa ccccatctct
 cctaaaaata gaaaaaaaag aattagctgg gcgtggtggt acatgcctgt aatcccatct
 cctcagaagg ctgaggcagg agaatcgctt gagcctcgga ggtggaggtt gcagtgagcc
 aagattgtgc cactgcactc cagcctgggt gacagagtga gactccatct aaaaaaaaat
 gaaaaaCAGT Agggatacgt ctgagcaatg tgtcctcagg caatttgtca ttgtgcaagg
 atcatagagt gtgtttacac aaacctacat gaaataccct gctacaccca ggctgtgtgg
 gatagcatag tgctcctagg taacaaatct gtatgtcatg taagtgtact aaatactgtg
 ggcagctgaa tcaccatagt agatgtttat acagatgaac atatctaagc atggaaaaaa
 tgcagtgaaa atacagtatt ataatctaat gagacctttg tcatgtatgt gg
 Y
 ctgttgttca cccaaatatc aaaatgtgca tgattCtatt caagttgctg aaaaaaaaag
 ccaaaaaact tccaaataaa tatcttacag ggattaaagc ttttcttcag taatgcagga
 tgtttgagaa gtttcccaaa aaagtaaaaa gtcgacaagt tcatcaccac taggccggcc
 ttacaggaaT GCCAAGTGTC TCTGGCAGGT TTCCTGAACA AGGAAGTAGC TGCATCAGCT
 CCACTCTGTT ATCTGCCAAT TGATAGATTT GCATAGTTTT TAATTTTAAT TTCTCTTCTG
 TTTTTTCCCT CCATAAACTC CTTCTCCCTT CCTTTCATAA TTCTGTCTAT TAATGCAACT
 CATATTTAGC TGACAATGCT GGGGTCAT

  GeneView back to top
GeneView via analysis of contig annotation: LOC642131 similar to hCG1812074
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_077631->XM_001716834
svfunction
CeleraNW_925606->XM_001717736
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_077631->XM_001716834->XP_001716886208430reverse3' near gene
CeleraNW_925606->XM_001717736->XP_00171778810571forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs6602939 maps exactly once on NCBI human chromosome 15
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
15NW_925606.110571165426minusGalt_assembly_1CeleraCeleraview1132
15NW_001838187.216929869342minusAalt_assembly_8HuRefHuRefview1132
15NW_001838188.2142246888108minusAalt_assembly_8HuRefHuRefview1132
15NT_077631.120843019971908plusCref_assemblyreferencereferenceview1132

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_077631
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC025884.28 AC134979.5 AC134981.6 AC135068.5 NC_000015.8 AC060768.3 AC134780.5

  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
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .