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dbSNP
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Reference SNP (refSNP) Cluster Report: rs59306077                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:129/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/AT (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:-=0.2332/1168 (1000 Genomes)
-=0.2364/29689 (TOPMED)
HGVS Names
  • CM000663.2:g.833759_833760delAT
  • NC_000001.10:g.769139_769140delAT
  • NC_000001.11:g.833759_833760delAT
  • NR_015368.2:n.287+4655_287+4656delAT
  • NR_047519.1:n.287+4655_287+4656delAT
  • NR_047520.1:n.287+4655_287+4656delAT
  • NR_047521.1:n.287+4655_287+4656delAT
  • NR_047522.1:n.287+4655_287+4656delAT
  • NR_047523.1:n.287+4655_287+4656delAT
  • NR_047524.1:n.287+4655_287+4656delAT
  • NR_047525.1:n.154+4655_154+4656delAT
  • NR_047526.1:n.287+4655_287+4656delAT
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 ss287939301 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs59306077 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
ss83547739HGSV|Cor18517_DIV_20070510.chr1_809001-809004_1fwd/-/ATaagatgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacggctgag12/04/0712/05/07129Genomicunknown
ss287939301GMI|GMI_AK_INDEL_62fwd/-/ATaagatgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacggctgag12/20/1012/22/11137Genomicunknown
ss3259974441000GENOMES|JPTCHB_chr1_759001_indelfwd/-/ATaagatgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacggctgag03/11/1104/01/11135Genomicunknown
ss4987638281000GENOMES|20110316_indels_chr1_769138_769139fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg03/19/1203/19/12137Genomicunknown
ss550899127LUNTER|YRI_1_759002-759003fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg11/21/1211/21/12138Genomic95 %
ss550903122LUNTER|CEU_1_759002-759003fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg11/21/1211/21/12138Genomic95 %
ss552738987LUNTER|JPTCHB_1_759002-759003fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg11/21/1211/21/12138Genomic95 %
ss553708523TISHKOFF|del_chr1_769139-769140fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg11/22/1211/22/12138Genomicunknown
ss663205229SSMP|indel_1_769139fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg12/18/1202/09/15144Genomicunknown
ss666079984BILGI_BIOE|indel_1_769139-769140fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg12/26/1212/26/12138Genomicunknown
ss974769350EVA-GONL|EVA-GONL_rs59306077fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg04/23/1404/23/14142Genomicunknown
ss13676453771000GENOMES|PHASE3_V1_4005byFreqfwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg08/16/1408/07/15142Genomicunknown
ss1573867864EVA_GENOME_DK|EVA_GENOME_DK_gatk_indels_rs59306077fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg02/19/1502/19/15144Genomicunknown
ss1584129484EVA_DECODE|EVA_DECODE_1_759001_222_rs59306077fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg03/02/1503/02/15144Genomicunknown
ss1700142320EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_769138_283fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg03/04/1503/06/15144Genomicunknown
ss1700153430EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_769138_283fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg03/04/1503/06/15144Genomicunknown
ss1793705773HAMMER_LAB|Hsieh_207fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg07/15/1507/15/15146Genomicunknown
ss2030297730JJLAB|INDEL64fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg08/30/1608/31/16149Genomicunknown
ss2750638531GNOMAD|rs762168062fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg05/17/1705/17/17151Genomicunknown
ss2986149012SWEGEN|NC_000001.10:769139_769140delfwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg05/30/1705/30/17151Genomicunknown
ss3063573495MCHAISSO|HG0051491fwd/-/ATgcaaagcatatggctctggtgagacgtgtgaggagctgagaatgagacgg09/15/1709/15/17151Genomic92 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs59306077|allelePos=501|totalLen=1001|taxid=9606|snpclass=2|alleles='-/AT'|mol=Genomic|build=151
 TTCCTAACTT ACTTTCCAGG GGATCGTTCC TGACTTAACA TCTATCAGGT GTCTTAGCTT
 AGCTCTCTTT TTACTTCAGG TTTTTCTTGC CTCCTCAGTG TGCTGGGAGT CCCACTCCAC
 TCAAATGCCC TCAGGTCTAA TAATTAACTT CATTGCAGGC TCCTGGCAGG CCTGGGTGGG
 CGGCAGCTGC ATTGTGCTCC TGAAGAAGAT TTAAGTTGGG TTTGGTGAAC TGGTAGAATT
 TGCATTTTGC TGTTTCTTTC CCTCTCCCAG AATTTGTACC TTTAAATAGG TTTTTTAGTG
 TCATTAAGTA TATCAAAAGG AAACCCAGTG GGGCAAATTG GCCGGGCTCC ATAGAGGTGG
 CCTTGTCTAA GCCTTTCATC TTATCGATAA GGAAAGACAG GACCAGAGAA GTCGCCGACT
 GTCCCTGGTC CCACTGCTTG GTTTGGGGCA ATTTCCTGAA AATAATATCC AAGATGCAAA
 GCATATGGCT CTGGTGAGAC
 N
 GTGTGAGGAG CTGAGAATGA GACGGCTGAG TGTCGGGGGC AGATCACGAA GGGCTGCGCT
 CACCATCAGG AGGTCTGGAC TTCGCTGTGA AAGACACAGG CCCTCATGTA CGTCCAGGAT
 GCGGTGACAG CGAGGCTTGC AGGAGACAGG TCCCTGCTGT GTGGGGGTGA AGCTGGAGGC
 AAGATGATGC CTGGAGCTAA GAGATGGTCA CAGGAAATCC GGCAAGAATT AACGAGGACT
 GGACAGTGAC AGGCAGGCCA AAGAGTGAGA GGAACTTCAC TGGCAAGAGC CAACAGGGCT
 TGTTGATTTA GGAGAGGAGA CAAAGGACTG AGGGGTTTGG GGGCTGGGGC CTGGGAGGGT
 GGAGAAGCCA CTGTCTGCAT TATGGGATGC AGGAGGAGAA GCATTCAGTT CTCCACACAA
 TGAGTTCCCT GAGAGGTGTC TCAGTGGGAT CGTGGTGCAG TTGGAAATGT TCATGAGAAA
 GATGAGAAGC GGCACCAGCA

  NCBI Resource Links back to top
Submitter-Referenced
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.
SourceHWP-
AT
ss1367645377EAS 1008AF 0.104200000.89579999
EUR 1006AF 0.124300000.87570000
AFR 1322AF 0.493199970.50680000
AMR 694AF 0.168599990.83139998
SAS 978AF 0.172800000.82720000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.358+/-0.2260000

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