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Reference SNP (refSNP) Cluster Report: rs202196885                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:137/147
Map to Genome Build:107/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/TCCTTAAG (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:-=0.0401/201 (1000 Genomes)
HGVS Names
  • NC_000023.10:g.448994_449001delTCCTTAAG
  • NC_000023.11:g.488259_488266delTCCTTAAG
  • NC_000024.10:g.488259_488266delTCCTTAAG
  • NC_000024.9:g.398994_399001delTCCTTAAG
  • NT_187634.1:g.171612_171619delTCCTTAAG
  • NT_187667.1:g.160752_160759delTCCTTAAG
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 ss499904087 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs202196885 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
ss4999040871000GENOMES|20110316_indels_chrX_448993_449000fwd/-/TCCTTAAGgttacccatgaaatctaagcttggtcctcgcctctttgaagaggaatcca03/19/1203/20/12137Genomicunknown
ss555048476TISHKOFF|del_chrX_448994-449001fwd/-/TCCTTAAGgttacccatgaaatctaagcttggtcctcgcctctttgaagaggaatcca11/22/1211/23/12138Genomicunknown
ss15532410461000GENOMES|PHASE3_chrX_14870byFreqfwd/-/TCCTTAAGgttacccatgaaatctaagcttggtcctcgcctctttgaagaggaatcca08/16/1408/07/15144Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs202196885|allelePos=26|totalLen=51|taxid=9606|snpclass=2|alleles='-/TCCTTAAG'|mol=Genomic|build=144
 GTTACCCATG AAATCTAAGC TTGGT
 N
 CCTCGCCTCT TTGAAGAGGA ATCCA

  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 AscertainmentGenotypesAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceHWP-
TCCTTAAG
ss1553241046EAS 1008AF 0.001000000.99900001
EUR 1006AF 1.00000000
AFR 1322AF 0.147499990.85250002
AMR 694AF 0.007200000.99279994
SAS 978AF 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.077+/-0.1810000

  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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