NCBI
dbSNP
Attention: This page will be retired!
This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
Spacer gif

Spacer gif
Reference SNP (refSNP) Cluster Report: rs116801199                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:132/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.0359/180 (1000 Genomes)
T=0.0372/4666 (TOPMED)
HGVS Names
  • CM000663.2:g.785001G>T
  • NC_000001.10:g.720381G>T
  • NC_000001.11:g.785001G>T
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 ss230395403 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs116801199 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
ss2303954031000GENOMES|pilot_1_CEU_32_chr1_710244fwd/G/Ttaaaaaatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatattctaca05/01/1005/01/10132Genomicunknown
ss2381149401000GENOMES|pilot_1_CHB+JPT_17_chr1_710244fwd/G/Ttaaaaaatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatattctaca05/01/1005/01/10132Genomicunknown
ss647515864SSMP|1_720381fwd/BG/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt12/14/1202/09/15138Genomicunknown
ss974769066EVA-GONL|EVA-GONL_rs116801199fwd/BG/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt04/23/1404/23/14142Genomicunknown
ss12893380111000GENOMES|PHASE3_V1_2687fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt08/16/1408/16/14142Genomicunknown
ss1584129344EVA_DECODE|EVA_DECODE_1_710244_82_rs116801199fwd/BG/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt03/02/1503/02/15144Genomicunknown
ss1599378234EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_720381_82fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt03/04/1503/04/15144Genomicunknown
ss1642372267EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_720381_82fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt03/04/1503/04/15144Genomicunknown
ss1917959745WEILL_CORNELL_DGM|SNV:chr1:720381fwd/BG/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt10/16/1510/16/15147Genomicunknown
ss2019498271JJLAB|SNP826fwd/BG/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt08/29/1608/30/16149Genomicunknown
ss2697374033GRF|rs116801199fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt02/13/1702/13/17151Genomicunknown
ss2750633252GNOMAD|rs116801199fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt05/17/1705/17/17151Genomicunknown
ss2986147760SWEGEN|NC_000001.10:g.720381G>Tfwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt05/30/1705/30/17151Genomicunknown
ss3343272190CSHL|rs116801199fwd/G/Taatgaatctaataatgaggaaacatagaaaaaaccaaactgagggatatt10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs116801199|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 AATTATGTAT TACTTACAAA GGGGAAAAGT GCACCTTGAC GTGAGAATCT TGGCAGAACT
 ACTTTAATCA AGAGGTTTAG TTGAGCATTA TCAGTAACAG AGTAAATCAA AATCATAAGC
 CACTTGATAG ATACAATGAG AAAATAAAGC ATCACTTCTG TGACACCCTA TAAAAAATGA
 ATCTAATAAT GAGGAAACAT
 K
 AGAAAAAACC AAACTGAGGG ATATTCTACA AATAAATTGT CCTGTAATCT TCAAAAATTT
 CAAGGTTATA AAAGTCAAGA AAAACAGACA ATCTTTTCCA AACTCAAGGG AACTAAAGAG
 GCATGAAATC TAAATGCTTA ATTCTGGATT TCATCTTTTT GATATAAAGA ACAGTATTGA
 GACTATTGAT AAAATTTGAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
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.
SourceHWPG
T
ss1289338011EAS 1008AF 0.962300000.03770000
EUR 1006AF 0.955299970.04470000
AFR 1322AF 0.974300030.02570000
AMR 694AF 0.971200050.02880000
SAS 978AF 0.956000030.04400000
ss230395403pilot_1_CEU_low_coverage_panel 120AF 0.958333310.04166667
ss238114940pilot_1_CHB+JPT_low_coverage_panel 120AF 0.899999980.10000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.069+/-0.1730000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN