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Reference SNP (refSNP) Cluster Report: rs3118454                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.00005/5 (ExAC)
A=0.00002/3 (TOPMED)
HGVS Names
  • CM000663.2:g.25301672G>A
  • NC_000001.10:g.25628163G>A
  • NC_000001.11:g.25301672G>A
  • NG_007494.1:g.34183G>A
  • NM_001127691.2:c.787G>A
  • NM_001282867.1:c.289G>A
  • NM_001282868.1:c.787G>A
  • NM_001282869.1:c.787G>A
  • NM_001282870.1:c.787G>A
  • NM_001282871.1:c.787G>A
  • NM_001282872.1:c.787G>A
  • NM_001321772.1:c.-67+35368C>T
  • NM_016124.4:c.787G>A
  • NP_001121163.1:p.Gly263Arg
  • NP_001269796.1:p.Gly97Arg
  • NP_001269797.1:p.Gly263Arg
  • NP_001269798.1:p.Gly263Arg
  • NP_001269799.1:p.Gly263Arg
  • NP_001269800.1:p.Gly263Arg
  • NP_001269801.1:p.Gly263Arg
  • NP_057208.2:p.Gly263Arg
  • NR_135787.1:n.1215+35368C>T
  • NR_135788.1:n.277+36306C>T
  • NR_135789.1:n.1215+35368C>T
  • XP_005246016.1:p.Gly263Arg
  • XP_005246017.1:p.Gly263Arg
  • XP_005246018.1:p.Gly263Arg
  • XP_005246019.1:p.Gly263Arg
  • XP_005246020.1:p.Gly263Arg
  • XP_016857504.1:p.Gly263Arg
  • XR_946736.1:n.942G>A
  • XR_946737.1:n.942G>A
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 ss163999042 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3118454 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
ss4361834SC_JCM|AL139426.15_168957byFreqfwd/BC/Tgcagcgccctgctcaccttgctgatcttccttgggggtgagccaaggatgaccctgagat02/19/0203/31/08103Genomicunknown
ss163999042COMPLETE_GENOMICS|NA07022_36_chr1_25500750rev/TA/Gatctcagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggcgctgc09/28/0909/29/09132Genomicunknown
ss3284846361000GENOMES|20100804_snps_128172_chr1_25628163rev/A/Gatctcagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggcgctgc03/22/1103/22/11134Genomicunknown
ss1685398849EVA_EXAC|EVA_EXAC_194672rev/A/Gagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggc03/04/1503/04/15144Genomicunknown
ss2731264856GNOMAD|exomes_rs3118454rev/A/Gagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggc05/17/1705/17/17151Genomicunknown
ss2746262138GNOMAD|coding_rs3118454rev/A/Gagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggc05/17/1705/17/17151Genomicunknown
ss2752823016GNOMAD|rs3118454rev/A/Gagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggc05/17/1705/17/17151Genomicunknown
ss3071294166TOPMED|TOPMed_freeze_5?chr1:25,301,672rev/A/Gagggtcatccttggctcacccccaaggaagatcagcaaggtgagcagggc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3118454|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GGATGGATTT AATCACTACC CCCAGAAAGC CTTTGATCAC TGGACAGTCT CCTGAGTCCC
 AGGCCCACTG TGACCACCCA GCATTCTACC TAGAGCTCCA CTGTAGAGGC AGGCACAGCT
 CCACCACCCG GCATGCCCTC TCCCAACCCA CGCTGGCCCT GGGGTGGGGA GGGGCATAAA
 TATGTGTGCT AGTCCTGTTA GACCCAAGTG CTGCCCAAGG GCAGCGCCCT GCTCACCTTG
 CTGATCTTCC
 Y
 TTGGGGGTGA GCCAAGGATG ACCCTGAGAT GGCTGTCACC ACGCTGACTG CTACAGCATA
 GTAGGTGTTG AACACGGCAT TCTTCCTTTC GATTGGACTT CTCAGCAGAG CAGAGTTGAA
 ACTTGGCCAG AACATCCACA AGAAGAGGGC GCCTGGGGGC CAGAGAGGGT GGTTGGCCAG
 AATCACACTC CTGCTCCAAA GGTCTGAGCC TCGAGGGGTT TTGGATGAGA ATCCTAGGGC
 TGGAGAGTCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001 AL031284
dbSNP Blast Analysis
UniGene Cluster ID
269364
3D structure mapping
NP_001121163  NP_057208  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3118454 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
HWPC
T
ss163999042CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss1685398849ExAc_Aggregated_Populations112346AF 0.999955480.00004451
ss4361834HapMap-CEUEuropean 112IG0.875000000.125000001.000000000.937500000.06250000
HapMap-HCBAsian 88IG1.00000000 1.00000000
HapMap-JPTAsian 86IG1.00000000 1.00000000
HapMap-YRISub-Saharan African 116IG0.948275860.051724141.000000000.974137900.02586207
ENSEMBL_Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0070000

  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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