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Reference SNP (refSNP) Cluster Report: rs116425261                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.000008/1 (ExAC)
G=0.0002/1 (1000 Genomes)
HGVS Names
  • CM000663.2:g.17632431C>G
  • NC_000001.10:g.17958926C>G
  • NC_000001.11:g.17632431C>G
  • NG_050860.1:g.117235C>G
  • NM_001011722.2:c.1578C>G
  • NM_001319837.1:c.1578C>G
  • NM_001319838.1:c.819C>G
  • NM_001328124.1:c.1029C>G
  • NM_018125.3:c.1695C>G
  • NP_001011722.2:p.Leu526=
  • NP_001306766.1:p.Leu526=
  • NP_001306767.1:p.Leu273=
  • NP_001315053.1:p.Leu343=
  • NP_060595.3:p.Leu565=
  • NR_137287.1:n.1857C>G
  • NR_137288.1:n.1737C>G
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 ss217411032 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs116425261 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
ss2174110321000GENOMES|pilot_3_YRI_30_chr1_17831513fwd/C/Gtaagtccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaacatcaac04/09/1004/09/10132Genomicunknown
ss3284486051000GENOMES|20100804_snps_92141_chr1_17958926fwd/C/Gtaagtccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaacatcaac03/22/1103/22/11134Genomicunknown
ss4897248151000GENOMES|20110521_exome_296462_chr1_17958926fwd/C/Gtaagtccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaacatcaac02/10/1202/21/12137Genomicunknown
ss534958149ILLUMINA|HumanOmni5-4v1_B_kgp25300501-0_B_F_1880890183fwd/C/Gccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaaca06/22/1208/28/15146Genomicunknown
ss12898663881000GENOMES|PHASE3_V1_552039fwd/C/Gccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaaca08/16/1408/16/14142Genomicunknown
ss1685351026EVA_EXAC|EVA_EXAC_143715fwd/C/Gccaaggagcgtcgggtcttcctgctaacgacatgcttgtctgtgccaaca03/04/1503/04/15144Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs116425261|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=146
 TTTCTGCACC ATGGGAGGAT TCTGGGTCTC CGGCGCGGTA AAGCCGCCGG GCCGCGATGC
 TGATGCTGAC CTTCCCTGCC CCTCCTCCAG CTGTTGACCT CAGGCCAGCG GCAGCTGCTC
 CTGTGTGAGA CGTTGACGGA GACCGTGTAC GGTGACCGCG GGCAGCTAAT TAAGTCCAAG
 GAGCGTCGGG TCTTCCTGCT
 S
 AACGACATGC TTGTCTGTGC CAACATCAAC TTCAAGTAAG TGGGCCTGGG TTGGAGGGGG
 CAATCACCCC TCCCTGGAGA CCCCATCCCG CCCTACTCCA GTCTCTTGGC CGGCCGCACT
 ACAGTGGGAC CCCATGTGAG CTTGGTTTAG GCTTCCAATA TTCCTCTCCC ATCCCTCTTG
 CCCTGCTCTG CCACTGGTCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
NP_001011722  NP_060595  

  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
G
ss1289866388EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.999199990.00080000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685351026ExAc_Aggregated_Populations121412AF 0.999991770.00000824
ss217411032pilot_3_YRI_exon_capture_panel 186AF 0.994623660.00537634

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0030000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN