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Reference SNP (refSNP) Cluster Report: rs881153                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Clinical Channel:unknown
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.006/14
MAF Source:1000 Genomes
HGVS Names
  • NC_000005.10:g.172772744C>T
  • NM_004417.3:c.-1792G>A
  • NT_023133.14:g.17011420C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence 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 ss1307586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs881153 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
ss1307586TSC-CSHL|TSC0216955byFreqfwd/TA/Gctctttgctgtcctcgaccaatgttcaaataaggtagaagacgcccttttaaaaaaaaaa09/06/0004/07/0486Genomic95 %
ss6061255SC_JCM|NT_023132.9_4152179rev/BC/Tttttttttttaaaagggcgtcttctaccttatttgaacattggtcgaggacagcaaagag01/10/0310/10/03111Genomicunknown
ss44641336ABI|hCV8953136rev/BC/Tttttttttttaaaagggcgtcttctaccttatttgaacattggtcgaggacagcaaagag07/19/0507/19/05126Genomicunknown
ss2221236061000GENOMES|pilot_1_YRI_3933289_chr5_172132353rev/C/Tttttttttttaaaagggcgtcttctaccttatttgaacattggtcgaggacagcaaagag04/22/1004/22/10132Genomicunknown
ss558897739TISHKOFF|snp_chr5_172199747rev/BC/Ttttttaaaagggcgtcttctaccttatttgaacattggtcgaggacagca11/22/1211/23/12138Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs881153|allelePos=102|totalLen=646|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=138
 ATAAGTAGTA TAAACAATTT CTTTTTCTTC TATCTCTCCA TACAGGGAGG GCGTTGCCCT
 TATCTGAGGA CCTCTTTGCT GTCCTCGACC AATGTTCAAA T
 R
 AAGGTAGAAG ACGCCCTTTT AAAAAAAAAA GCACTCCATG CCCTGAACTT TTCTAGAAGA
 ATCCAGGCAG AACATTTGCG CAGGCGAAAA CACACAAGCT AAGCGAGGCA AATGCAGAAG
 TTGCCACTGG TGATACAGCT CGCACAGCGA CGACGCAGGG TGGCCAGCGA AATCCCCTCC
 CCCAGGAGGG GAGGAAACCG CAGAATGTTC CTGACTCGGC ACCCGGGCGG GTGGCGCAAT
 GTTTATGTTT GTGTACCTAG CGCGTCGCGT CGCTGCAGCA GGCTCCGCTG TCCAGGGGGC
 CGTCACTGGG ACTCAGGGCA CGGAGATCGC TGGGCGGGGC GGGGGTCTTC CCAAGTGTTG
 CGATCCAGGT CCTGGCAATC CGCCCACAAT GGCCCGGGAT TGGATTTTGC TTTCGGCCTA
 TAACGGCCGC GACGACAGGG AGCGAGGGTT GTGGCCGGCT TCTGTTCCGG GTTGGAGGCC
 CCCCAGCCCA GCGCTTTAGT GGCGCTCACT GTGTATACTG CCTATTTGTA TATAAAAAAA
 GGGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023132.9 AC022217.3
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWPA
G
ss1307586TSC_42_AA 78AF 0.030 0.970
TSC_42_C 80AF 1.000
TSC_42_A 82AF 0.040 0.960
CEPH 184AF 1.000
ss222123606pilot_1_YRI_low_coverage_panel 118AF 0.042 0.958

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.013+/-0.0790000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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