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Reference SNP (refSNP) Cluster Report: rs17418085                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.0066/718 (ExAC)
C=0.0268/134 (1000 Genomes)
C=0.0101/120 (GO-ESP)
C=0.0208/2616 (TOPMED)
HGVS Names
  • CM000663.2:g.25290760A>C
  • NC_000001.10:g.25617251A>C
  • NC_000001.11:g.25290760A>C
  • NG_007494.1:g.23271A>C
  • NM_001127691.2:c.455A>C
  • NM_001282867.1:c.-40A>C
  • NM_001282868.1:c.455A>C
  • NM_001282869.1:c.455A>C
  • NM_001282870.1:c.455A>C
  • NM_001282871.1:c.455A>C
  • NM_001282872.1:c.455A>C
  • NM_001321772.1:c.-66-43731T>G
  • NM_016124.4:c.455A>C
  • NP_001121163.1:p.Asn152Thr
  • NP_001269797.1:p.Asn152Thr
  • NP_001269798.1:p.Asn152Thr
  • NP_001269799.1:p.Asn152Thr
  • NP_001269800.1:p.Asn152Thr
  • NP_001269801.1:p.Asn152Thr
  • NP_057208.2:p.Asn152Thr
  • NR_135787.1:n.1216-43731T>G
  • NR_135788.1:n.278-43731T>G
  • NR_135789.1:n.1216-43731T>G
  • XP_005246016.1:p.Asn152Thr
  • XP_005246017.1:p.Asn152Thr
  • XP_005246018.1:p.Asn152Thr
  • XP_005246019.1:p.Asn152Thr
  • XP_005246020.1:p.Asn152Thr
  • XP_005246021.1:p.Asn152Thr
  • XP_016857504.1:p.Asn152Thr
  • XR_946736.1:n.610A>C
  • XR_946737.1:n.610A>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 ss341945887 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17418085 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
ss341945887NHLBI-ESP|ESP2500-chr1-25617251byFreqfwd/TA/Ctggtgctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatcttcaa03/25/1109/05/14137Genomicunknown
ss4886579481000GENOMES|20110521_exome_5794_chr1_25617251fwd/TA/Ctggtgctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatcttcaa02/10/1202/13/12137Genomicunknown
ss491289430EXOME_CHIP|nonsyn_5657_chr_1_25617251fwd/TA/Ctggtgctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatcttcaa03/05/1203/05/12137Genomicunknown
ss491589281CLINSEQ_SNP|SNV-chr1-25489838fwd/TA/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc03/06/1203/12/12137Genomicunknown
ss974960279EVA-GONL|EVA-GONL_rs17418085fwd/TA/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc04/23/1404/23/14142Genomicunknown
ss12900891181000GENOMES|PHASE3_V1_783445fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc08/16/1408/16/14142Genomicunknown
ss1425750410DDI|DDI_rs17418085fwd/TA/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc11/04/1411/04/14144Genomicunknown
ss1685398739EVA_EXAC|EVA_EXAC_194550fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc03/04/1503/04/15144Genomicunknown
ss1918172061WEILL_CORNELL_DGM|SNV:chr1:25617251fwd/TA/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc10/16/1510/16/15147Genomicunknown
ss2731264708GNOMAD|exomes_rs17418085fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc05/17/1705/17/17151Genomicunknown
ss2746262092GNOMAD|coding_rs17418085fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc05/17/1705/17/17151Genomicunknown
ss2752822169GNOMAD|rs17418085fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc05/17/1705/17/17151Genomicunknown
ss3071292322TOPMED|TOPMed_freeze_5?chr1:25,290,760fwd/A/Cctggtggaggtgacagctttaggcacctgaggatggtcatcagtaatatc09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs17418085|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 CTTCTATTCC CACAGAAAGT AGGTGCCCAA CAGTGTTTGT TGAAAGAATG AATGAATGAA
 TGAATGAATG AATGAATGAG TGAGAGGCAT CCTTCCTTCT CAGTCGTCCT GGCTCTCCCT
 CTCTCCCCCA GTATTCGGCT GGCCACCATG AGTGCTTTGT CGGTGCTGAT CTCAGTGGAT
 GCTGTCTTGG GGAAGGTCAA CTTGGCGCAG TTGGTGGTGA TGGTGCTGGT GGAGGTGACA
 GCTTTAGGCA
 M
 CCTGAGGATG GTCATCAGTA ATATCTTCAA CGTGAGTCAT GGTGCTGGGA GGAGGGACCT
 GGGAGAAAAG GGCCAAAAGC TCCATTTGGT GGGGTTTCCA GGGTTTTGAA AAATAAAGAC
 AACCTGTAAT CCCAGCTACT TGGGAGGTTG AGGAGGGAAG ATCACTTGAG GCCAGGAGTT
 TGAGACCAGC CTGGGCATCA TAGCAAGATC CTCATCTCTA AAAAGTAATT TTTTCTAAAT
 TATCCAGTTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001
dbSNP Blast Analysis
UniGene Cluster ID
269364
3D structure mapping
NP_001121163  NP_057208  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss1290089118EAS 1008AF 1.00000000
EUR 1006AF 0.988100050.01190000
AFR 1322AF 0.917500020.08250000
AMR 694AF 0.989899990.01010000
SAS 978AF 0.993900000.00610000
ss1685398739ExAc_Aggregated_Populations112554AF 0.993505360.00649466
ss341945887ESP_Cohort_Populations 4026GF0.974664690.015896670.009438650.001000000.982613030.01738698
ss491589281CSAgilent 1101GF0.998000030.00200000 1.000000000.999000010.00100000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.013+/-0.0800000

  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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