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Reference SNP (refSNP) Cluster Report: rs199814742                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:137/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:A:germline
G:germline
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:G=0.0139/215 (ExAC)
G=0.0011/4 (1000 Genomes)
G=0.0035/34 (GO-ESP)
G=0.0030/381 (TOPMED)
HGVS Names
  • CM000685.2:g.18564539A>G
  • NC_000023.10:g.18582659A>G
  • NC_000023.11:g.18564539A>G
  • NG_008475.1:g.143935A>G
  • NM_001037343.1:c.145+17A>G
  • NM_001323289.1:c.145+17A>G
  • NM_003159.2:c.145+17A>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 ss489225277 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs199814742 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
ss4892252771000GENOMES|20110521_exome_285843_chrX_18582659fwd/TA/Gcaaggacagtgaaggtagatatatatatattatatatatatctgtatatatgtatttttc02/10/1202/14/12137Genomicunknown
ss538296220CHWRETT|145+17A>Gfwd/TA/Gcaaggacagtgaaggtagatatatatatattatatatatatctgtatatatgtatttttc08/08/1208/08/12137Genomicunknown
ss713644538NHLBI-ESP|ESP6500SI-chrX-18582659fwd/TA/Gcaaggacagtgaaggtagatatatatatattatatatatatctgtatatatgtatttttc02/20/1302/20/13138Genomicunknown
ss15536861651000GENOMES|PHASE3_chrX_459989byFreqfwd/TA/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat08/16/1408/07/15144Genomicunknown
ss1583339725EVA_GENOME_DK|EVA_GENOME_DK_snv_rs199814742fwd/TA/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat02/19/1502/20/15144Genomicunknown
ss1694468419EVA_EXAC|EXAC_0.3.X:g18582659a>gfwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat03/04/1503/04/15144Genomicunknown
ss1939182531WEILL_CORNELL_DGM|SNV:chrX:18582659fwd/TA/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat10/16/1510/19/15147Genomicunknown
ss2316002900HUMAN_LONGEVITY|HLI-X-18564539-A-Gfwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat11/18/1611/18/16150Genomicunknown
ss2745323245GNOMAD|exomes_rs199814742fwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat05/17/1705/17/17151Genomicunknown
ss2746082197GNOMAD|coding_rs199814742fwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat05/17/1705/17/17151Genomicunknown
ss2976932905GNOMAD|rs199814742fwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat05/23/1705/23/17151Genomicunknown
ss3019694715SWEGEN|NC_000023.10:g.18582659A>Gfwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat05/30/1705/30/17151Genomicunknown
ss3606381613TOPMED|TOPMed_freeze_5?chrX:18,564,539fwd/A/Gacagtgaaggtagatatatatatattatatatatatctgtatatatgtat10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs199814742|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CGGGGGAGAG GAAGATGATA TATTTTTAAC ACTCTGGCTT CTTGCTACTC TGTCCCAGAA
 TATACCCCCA GGCAACTGGA ATCCCCAGTC GGAAAAACAC TGGAGAATGA CTTTCCTTCT
 GCTTCTTTTC CCTTGCAGGA AACACATGAA ATTGTGGCGA TCAAGAAATT CAAGGACAGT
 GAAGGTAGAT ATATATATAT
 R
 TATATATATA TCTGTATATA TGTATTTTTC CTTCTGTATA AAGTTTTTAT ACATAGAGTG
 TGGAAGAAGT GGGATCTAGC TGGTCAGACA CTGTCTATTC CTGATATTTT GAAGTCACAA
 TCTCAGAAAG TGAATATAGC TTATTTCTTA TGCTTTGCTT TCAAACATTT AGTTCCTTTT
 ATGTGAATCT TTTCAAATCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000023
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.
SourceHWPA
G
ss1553686165EAS 1008AF 1.00000000
EUR 1006AF 0.995999990.00400000
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1694468419ExAc_Aggregated_Populations 76486AF 0.993868170.00613184

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.027+/-0.1140000

  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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