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Reference SNP (refSNP) Cluster Report: rs61249400                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/147
Map to Genome Build:107/Weight
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/A (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:-=0.0222/111 (1000 Genomes)
HGVS Names
  • NC_000001.10:g.174476084delA
  • NM_014857.4:c.1710+112801delA
  • XM_005245680.1:c.1710+112801delA
  • XM_005245681.1:c.1599+112801delA
  • XM_005245682.1:c.1536+112801delA
  • XM_005245683.1:c.1600-40891delA
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 ss193136519 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs61249400 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
ss193136519BUSHMAN|BUSHMAN-chr1-172742706-172742707fwd/-/Actgggcaacatggcgaaacctcatctctacaaaaaaatacaaaaattagctggatgtgga02/16/1002/16/10137Genomicunknown
ss4990395061000GENOMES|20110316_indels_chr1_174476083_174476083fwd/-/Acaacatggcgaaacctcatctctacaaaaaaatacaaaaattagctggat03/19/1203/19/12137Genomicunknown
ss551015388LUNTER|YRI_1_172742707-172742707fwd/-/Acaacatggcgaaacctcatctctacaaaaaaatacaaaaattagctggat11/21/1211/21/12138Genomic95 %
ss13678997411000GENOMES|PHASE3_V1_4311778byFreqfwd/-/Acaacatggcgaaacctcatctctacaaaaaaatacaaaaattagctggat08/16/1408/07/15142Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs61249400|allelePos=201|totalLen=401|taxid=9606|snpclass=2|alleles='-/A'|mol=Genomic|build=142
 ACCAAAATCT CTGAAATCAC TGCTAAAGAA CTTAATTCAT ATAACCAAAA ACCACCTGTT
 CCCCAAAAAC TATTGAAATA ATAGTAATAA AAAAAACTCA CACCTGTAAT CCTAGCACTT
 TGAAAGGCCA ATGTGGTTGG ATTGCTTGAG CTCAGAAGTT CGAGTCCACC CTGGGCAACA
 TGGCGAAACC TCATCTCTAC
 N
 AAAAAAATAC AAAAATTAGC TGGATGTGGA GGCGCGTGCC TGTGGTCCCA GCTACTTGGG
 GGGCTGAGGC GGGAGGATCC CTTGAGCCTG GGAGGCGGAA ACTTACCTTA TACACCATAA
 TTTTAATTTT TACTTGTCAA TTTAAAAAGA ATTTAAGGAA CAATGTTTGA AAATATGAGA
 AGAAATAGCT TAATAAATTG

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

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

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
Source-/A
HWP-
A
ss1367899741EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.080200000.91979998
AMR 694AF 0.007200000.99279994
SAS 978AF 1.00000000
ss193136519BUSHMAN_POP2 2IG1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.043+/-0.1410000

  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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