NCBI
dbSNP
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This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
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Reference SNP (refSNP) Cluster Report: rs117392462                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0010/5 (1000 Genomes)
T=0.00003/4 (TOPMED)
HGVS Names
  • CM000672.2:g.88750C>T
  • NC_000010.10:g.134690C>T
  • NW_003571043.1:g.78750C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

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


  Submitter records for this RefSNP Cluster back to top
The submission ss241753232 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs117392462 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
ss2417532321000GENOMES|pilot_1_CHB+JPT_3638309_chr10_124690fwd/C/Tcaatgctgggataattgggaaagacctacatctaagaatctgccttagagtgtaagacct05/01/1005/01/10132Genomicunknown
ss13359129481000GENOMES|PHASE3_V1_48502663fwd/C/Tctgggataattgggaaagacctacatctaagaatctgccttagagtgtaa08/16/1408/16/14142Genomicunknown
ss2171932784HUMAN_LONGEVITY|HLI-10-88750-C-Tfwd/C/Tctgggataattgggaaagacctacatctaagaatctgccttagagtgtaa11/18/1611/18/16150Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs117392462|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GTTGCAATGA ACTGAGATGG TGAGATGATG CCACTGCACT CAAGCCTGGG TGACGAGCAG
 GACCCCTGCC AAAAAACAAA GCCAGCAGGT CTGGGCTAAC CTTTAATTTC TTCTTCTATG
 AAGTGAGATA ATTGGACAAG ACATCTTTTA CAGGCAGCTC TAAAAGATTA CAATGCTGGG
 ATAATTGGGA AAGACCTACA
 Y
 TCTAAGAATC TGCCTTAGAG TGTAAGACCT ACACTCTTTC CAGGGACAGC CCTGAGGTAG
 ACAGGCTCTC TAGAAGATGG ACAGGCTCTC TAGAAGGTGG ACAGTCTCTC TAGAAGGTAG
 ACAGGCTCTC TAGAAGGTAG ACAGGCTCTC TAGAGGGTGG ACAGGCTCTC TAGAAGGTGG
 ACAGGCTCTC TAGAGGGTGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000010
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPC
T
ss1335912948EAS 1008AF 0.995000000.00500000
EUR 1006AF 1.00000000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss241753232pilot_1_CHB+JPT_low_coverage_panel 120AF 0.983333350.01666667

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.002+/-0.0320000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN