NCBI
dbSNP
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Reference SNP (refSNP) Cluster Report: rs116030099                 
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:C/T (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0413/207 (1000 Genomes)
C=0.0729/9157 (TOPMED)
HGVS Names
  • CM000663.2:g.787290T>C
  • NC_000001.10:g.722670T>C
  • NC_000001.11:g.787290T>C
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 ss283987304 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs116030099 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
ss2303954061000GENOMES|pilot_1_CEU_35_chr1_712533fwd/C/Taatttattcctacaatttcattctttttgaactagggtaaattgaattattttcttgatt05/01/1005/01/10132Genomicunknown
ss283987304GMI|GMI_NA10851_SNP_70fwd/C/Taatttattcctacaatttcattctttttgaactagggtaaattgaattattttcttgatt12/17/1012/17/10138Genomicunknown
ss974769080EVA-GONL|EVA-GONL_rs116030099fwd/BC/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct04/23/1404/23/14142Genomicunknown
ss12893380611000GENOMES|PHASE3_V1_2742fwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct08/16/1408/16/14142Genomicunknown
ss1573851065EVA_GENOME_DK|EVA_GENOME_DK_snv_rs116030099fwd/BC/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct02/19/1502/19/15144Genomicunknown
ss1584129355EVA_DECODE|EVA_DECODE_1_712533_93_rs116030099fwd/BC/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct03/02/1503/02/15144Genomicunknown
ss1599378237EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_722670_88fwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct03/04/1503/04/15144Genomicunknown
ss1642372270EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_722670_88fwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct03/04/1503/04/15144Genomicunknown
ss1917959770WEILL_CORNELL_DGM|SNV:chr1:722670fwd/BC/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct10/16/1510/16/15147Genomicunknown
ss2019498273JJLAB|SNP828fwd/BC/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct08/29/1608/30/16149Genomicunknown
ss2147483830USC_VALOUEV|NC_000001.10:g.722670T>Cfwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct11/17/1611/17/16150Genomicunknown
ss2750633427GNOMAD|rs116030099fwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct05/17/1705/17/17151Genomicunknown
ss2986147789SWEGEN|NC_000001.10:g.722670T>Cfwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct05/30/1705/30/17151Genomicunknown
ss3343272198CSHL|rs116030099fwd/C/Tattcctacaatttcattctttttgaactagggtaaattgaattattttct10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs116030099|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CTGTGTTTTC TTGATGTCCT TGTCAAAAAT TAGTTGACTT TTATATGCTT GGGTTTATTT
 CTGGGCTCTA TTCTGTTTCA TTGCTTTACA TCTCTGTTTT CATGCCAGTG CCACAGTGTT
 TTGATTACTA TAGCTTTGTA ATATAATTTG AAATCAGAAT GTGTAATACC TATAACTTTG
 TTTTTTGCTC TAAAGATTTA TTTATTTATT TATTTTTGCC ATTTCAGGTC TTTTGTGGTT
 TCATATGAAT TTCAGAATTG TTTTTCCTAT TTCTGTGAAA AATGCCATTG ACATTTTGAT
 AGGGATTGTG TTGAATCTAT ATATTGCTTT GGATAGTATG GATGTTTTAA CACTATTAAT
 TGTCCCAATC CATGAACATG AAATATCTTT CCATTCACTT GTGTCTTCTT CAATTTCTTT
 CATCAATGTT TTATAGTTTT CATTGTGCAG ATCTTTCACT TACCTGGTTA AATTTATTCC
 TACAATTTCA TTCTTTTTGA
 Y
 ACTAGGGTAA ATTGAATTAT TTTCTTGATT TCTATAAATT ATTTCTTATA ATACTCATAC
 TTGTCAGGCC TCTGGGCCCA AGCCTGCATG TATACATCCA GATGGCCTGA AATAACTGAA
 GAATCACAAA AGAAGTGAAA ATGGCCAGTT CCTGCCTTAA CTGGTGACAT TACCTTGTGA
 AATTCCTTCT CCTGGCTCAG AAGCTCCCCC GCTGAGCACC TTGTGACCCC CGTCCCTGCC
 CACCAGAGAA CAACCCCCTT TGACTGTAAT TGTCCACTAC CCACCCAAAT CCTATAAAAC
 AGCCCCACCC GTCTCCCTTC ACTGACTCCT TTTTCAGACT CAGCCTGCCT GCACCCAGGT
 GAAATAAACA GCCTTGTTGC TCACACAAAG CCTGTTGGTG GACTCTCTTC ACACAGATGC
 GCGAGACAAT ACTAACACTA ATATTATTTT GATTCGTCAG ATGGAAAAGT AAGGCTTGAA
 GAGGTTAGAA ATAACTTTTC

  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.
SourceHWPC
T
ss1289338061EAS 1008AF 0.002000000.99800003
EUR 1006AF 0.120299990.87970001
AFR 1322AF 0.006100000.99390000
AMR 694AF 0.083600000.91640002
SAS 978AF 0.018400000.98160005
ss230395406pilot_1_CEU_low_coverage_panel 120AF 0.066666670.93333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.079+/-0.1830000

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