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Reference SNP (refSNP) Cluster Report: rs66515830                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:130/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (REV)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.00003/4 (ExAC)
T=0.0002/1 (1000 Genomes)
T=0.00009/11 (TOPMED)
HGVS Names
  • CM000663.2:g.59911717A>T
  • NC_000001.10:g.60377389A>T
  • NC_000001.11:g.59911717A>T
  • NG_007931.1:g.20035T>A
  • NM_000775.3:c.575T>A
  • NP_000766.2:p.Ile192Asn
  • NR_134981.1:n.627T>A
  • NR_134982.1:n.627T>A
  • XR_246240.1:n.602T>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 ss105437687 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs66515830 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
ss105434281AFFY_DM3_1|DMET3B11627fwd/A/Ttcaagatcaacaatgcagtttccaatatcattgctccatcaccttcggagaacgctttga09/03/0809/03/08130Genomicunknown
ss105437687SNP500CANCER|CYP2J2-03byFreqfwd/A/Ttcaagatcaacaatgcagtttccaatatcattgctccatcaccttcggagaacgctttga09/05/0809/05/14130Genomicunknown
ss3286364861000GENOMES|20100804_snps_280022_chr1_60377389rev/A/Ttcaaagcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgatcttga03/22/1103/22/11134Genomicunknown
ss4897457571000GENOMES|20110521_exome_306850_chr1_60377389rev/A/Ttcaaagcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgatcttga02/10/1202/21/12137Genomicunknown
ss1067421912JMKIDD_LAB|HGDP_exomes_chr1_60377389rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat07/09/1407/09/14142Genomicunknown
ss12910345551000GENOMES|PHASE3_V1_1766646rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat08/16/1408/16/14142Genomicunknown
ss1685573632EVA_EXAC|EVA_EXAC_382427rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat03/04/1503/04/15144Genomicunknown
ss2325043070TOPMED|1_60377389_A/Trev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat11/19/1611/19/16150Genomicunknown
ss2710673008ILLUMINA|Consortium-OncoArray_15047405_A_rs66515830-131_T_R_2077149030rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat03/22/1703/22/17151Genomicunknown
ss2731538324GNOMAD|exomes_rs66515830rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat05/17/1705/17/17151Genomicunknown
ss2746343618GNOMAD|coding_rs66515830rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat05/17/1705/17/17151Genomicunknown
ss2755540566GNOMAD|rs66515830rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat05/17/1705/17/17151Genomicunknown
ss3077547183TOPMED|TOPMed_freeze_5?chr1:59,911,717rev/A/Tgcgttctccgaaggtgatggagcaatgatattggaaactgcattgttgat09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs66515830|allelePos=302|totalLen=602|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 AGTTTTAGAA GTAAATACAC AAAGATGGGC ACTAAACACA TTACTGAATT TAAGCCCTGG
 TCCGCAGTTT GACTTCCCTG GAGTTGACTG AATACTTGTT GTATGTCAGA TGCAGTGTAA
 GGTCATGTGG CCAGCTCCTC ATATATGGTT CTGCACTAGG TATGTCTTAT GCCATGTAAA
 GTAGACTCTC AGTAGGAAAT GGAGACAAAT CCATCAGAAG GATCCATCTT GCCCTTCCTC
 CACCTTCAGG ACAGCCTTTT GACCCTCANT TTCAAGATCA ACAATGCAGT TTCCAATATC
 A
 W
 TTGCTCCATC ACCTTCGGAG AACGCTTTGA GTACCAGGAT AGTTGGTTTC AGCAGCTGCT
 GAAGTTACTA GATGAAGTCA CATACTTGGA GGCTTCAAAG ACATGCCAGG TAAGGCAGCT
 GTCTCTCCAT ATCTTTGTTC AGTAAATTGG GGCCGATGTC AGCCACAGAT GGGTTTTTCC
 TTTTAGTTTT TTTTGGGTTT TTGAAGTTAA AATATAACCT TTCAAAACTA ATTTCAACAC
 AAACTTATTT GAAATMAATC TATTGACTTT AGTTTTTTAA CTAATATGGA ATATTTATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
3D structure mapping
NP_000766  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs66515830 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/T
T/T
HWPA
T
ss105437687P1 204GF0.019607840.980392161.000000000.009803920.99019605
CAUC1 62GF 1.00000000 1.00000000
AFR1 48GF0.083333340.916666691.000000000.041666670.95833331
HISP1 46GF 1.00000000 1.00000000
PAC1 48GF 1.00000000 1.00000000
ss1291034555EAS 1008AF 1.00000000
EUR 1006AF 1.00000000
AFR 1322AF 0.000800000.99919999
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1685573632ExAc_Aggregated_Populations121412AF 0.000032950.99996704

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.000+/-0.0060000

  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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