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Reference SNP (refSNP) Cluster Report: rs17538586                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/141
Map to Genome Build:106/Weight
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:unknown
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.017/37
MAF Source:1000 Genomes
HGVS Names
  • NC_000003.12:g.127611921G>T
  • NM_004526.3:c.1428+2898G>T
  • NR_073375.1:n.1557+2898G>T
  • NT_005612.17:g.33906347G>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 ss85447409 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17538586 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
ss28475046EGP_SNPS|MCM2-015514byFreqfwd/BG/Tgggtttcaccgttttagccgggatggtctcatctcctgacctcgtgatccgcccgcctcg07/13/0408/05/04123Genomicunknown
ss85447409HGSV|Cor19129_SNV_20070510.chr3_128813462fwd/BG/Tgggtttcaccgttttagccgggatggtctcatctcctgacctcgtgatccgcccgcctcg12/06/0712/09/07130Genomicunknown
ss4565129481000GENOMES|20101123_snps_2680178_chr3_127330764fwd/G/Tgggtttcaccgttttagccgggatggtctcatctcctgacctcgtgatccgcccgcctcg07/20/1107/20/11135Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17538586|allelePos=439|totalLen=939|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=135
 CCATCCCCAT GTGCTTCTGG AGCCCCAGGT TCCAAAACGA CTTGTTCCCC AAATGGAGGC
 AGCCCTACCC CGCTCCCGTG TCTTGATGCC TGCTATTTGT GTCTACATAG AGCACCTTCT
 CCCTCACTTG TCCCCAGCTG ACTTCTGTCT TCTGCAGATT CCATCTCCAG CAGGAAGCCC
 TGCAGGCTTC TGCAGCTGAC TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTGAGACG
 GAGTCTCGCT CTGTCGCCCA GGCTGGAGTG CAGTGGCGGG ATCTCGGCTC ACTGCAAGCT
 CCGCCTCCCG GGTTCACGCC ATTCTCCTGC CTCAGCCTCC CAAGTAGCTG GGACGACAGG
 CGCCCGCCAC TACGCCCGGC TAATTTTTTT GTATTTTTAG TAGAGACGGG GTTTCACCGT
 TTTAGCCGGG ATGGTCTC
 K
 ATCTCCTGAC CTCGTGATCC GCCCGCCTCG GCCTCCCAAA GTGCTGGGAT TACAGGCGTG
 AGCCACCGCG CCCGGCCAAC AGCTGACTTT TTGTATTTGT TTTTATTTTG AGTTAGTTAT
 CATCCTTGAG GGATCCGGAG ACTTCACATA GAAATCCGGA TGCTTTTTGA AAATCCAAGA
 TCTGTGGGTG CTGGCTCTGT GTTCCTCTCT GGTAACGCTG ACGGAGCTGA GGCATAGCTG
 CCCTTGCAGG TAGGGCCTGT GTCCCCAGGT TTACCCCGTC CCCTACTCTG TCAGTTTCAT
 GGCCCTGCCT GCCTTCCGTG GGCCCTGGAC ACTGATCTGG TAAAGTATTA AAGAGATCAG
 GGTCATGCCC AACACTTAGA GATTTTAAAG AACTAACAGA AGCAGCATGC AGTCTGAAGC
 CAGACTTTTT AGGTTTGAAT TTTGGCCTAA TCCTTAGGAT GGTCAGATGA GTCACCCTTA
 TCTATAGAAA TGAGAGGATG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000003
dbSNP Blast Analysis

  Population Diversity (in rs orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
G/T
HWPG
T
ss28475046PDR90Global 160IG 0.962 0.038 1.000 0.981 0.019
ss85447409ENSEMBL_Watson 2IG 1.000 1.000
ENSEMBL_Venter 2IG 1.000 1.000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.033+/-0.125929200

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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