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Reference SNP (refSNP) Cluster Report: rs1800940                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreq
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:G:germline
T:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:T=0.0007/88 (ExAC)
T=0.0011/14 (GO-ESP)
T=0.0012/150 (TOPMED)
HGVS Names
  • CM000665.2:g.46373082G>T
  • NC_000003.11:g.46414573G>T
  • NC_000003.12:g.46373082G>T
  • NG_012637.1:g.7941G>T
  • NM_000579.3:c.180G>T
  • NM_001100168.1:c.180G>T
  • NP_000570.1:p.Arg60Ser
  • NP_001093638.1:p.Arg60Ser
  • NR_125406.1:n.392-1665C>A
  • XP_005264911.1:p.Arg60Ser
  • XP_005264912.1:p.Arg60Ser
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 ss244238193 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800940 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
ss2421099HGBASE|SNP000063292fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc11/07/0010/10/0389Genomicunknown
ss76868266CGM_KYOTO|9650fwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc09/12/0709/12/07129cDNAunknown
ss95213604CNG|29947909fwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc03/13/0803/13/08130Genomicunknown
ss244238193OMICIA|2010_April_001_069_CCR5_601373_0008fwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc05/27/1005/28/10132Genomicunknown
ss263193955OMIM-CURATED-RECORDS|10140fwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc10/28/1010/28/10133Genomicunknown
ss342125133NHLBI-ESP|ESP2500-chr3-46414573byFreqfwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc03/25/1109/05/14134Genomicunknown
ss491338698EXOME_CHIP|nonsyn_54925_chr_3_46414573fwd/BG/Tggtcatcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacctgctc03/05/1203/05/12137Genomicunknown
ss780815969ILLUMINA|HumanOmni25Exome-8v1_A_exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/30/1307/09/15146Genomicunknown
ss783498151ILLUMINA|HumanOmniExpressExome-8v1_A_exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/31/1306/19/15146Genomicunknown
ss978547366EVA-GONL|EVA-GONL_rs1800940fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc04/23/1404/24/14142Genomicunknown
ss1584027227EVA_FINRISK|EVA_FINRISK_rs1800940fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc02/27/1502/27/15144Genomicunknown
ss1588016651EVA_DECODE|EVA_DECODE_3_46389577_394284_rs1800940fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc03/02/1503/03/15144Genomicunknown
ss1606974185EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_46414573_8344524fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc03/04/1503/04/15144Genomicunknown
ss1649968218EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_46414573_8344524fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc03/04/1503/04/15144Genomicunknown
ss1686966503EVA_EXAC|EVA_EXAC_1884158fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc03/04/1503/04/15144Genomicunknown
ss1752471713ILLUMINA|OmniExpressExome-8v1-1_B_exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/27/1506/09/15146Genomicunknown
ss1917766145ILLUMINA|HumanExome-12v1-1_B_exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc10/16/1510/16/15147Genomicunknown
ss1946081390ILLUMINA|HumanCoreExome-12v1-0_C_exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc10/29/1510/29/15147Genomicunknown
ss1958559328ILLUMINA|exm307645-0_B_F_1922102359fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc11/13/1511/13/15147Genomicunknown
ss2021455763JJLAB|SNP1958318fwd/BG/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc08/29/1608/30/16149Genomicunknown
ss2251182088HUMAN_LONGEVITY|HLI-3-46373082-G-Tfwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc11/18/1611/18/16150Genomicunknown
ss2418265745TOPMED|3_46414573_G/Tfwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc11/19/1611/19/16150Genomicunknown
ss2710971802ILLUMINA|Consortium-OncoArray_15047405_A_exm307645-0_B_F_1922102359fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc03/22/1703/22/17151Genomicunknown
ss2733690574GNOMAD|exomes_rs1800940fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/17/1705/17/17151Genomicunknown
ss2746990337GNOMAD|coding_rs1800940fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/17/1705/17/17151Genomicunknown
ss2792417158GNOMAD|rs1800940fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/18/1705/18/17151Genomicunknown
ss2985254163AFFY|Axiom_PsorMich_Affx-22374910fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/24/1705/24/17151Genomicunknown
ss2992240502SWEGEN|NC_000003.11:g.46414573G>Tfwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc05/30/1705/30/17151Genomicunknown
ss3022235365ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm307645-0_B_F_1922102359fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc06/28/1706/28/17151Genomicunknown
ss3389293199TOPMED|TOPMed_freeze_5?chr3:46,373,082fwd/G/Ttcctcatcctgataaactgcaaaagctgaagagcatgactgacatctacc10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800940|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 TGGAGGGCAA CTAAATACAT TCTAGGACTT TATAAAAGAT CACTTTTTAT TTATGCACAG
 GGTGGAACAA GATGGATTAT CAAGTGTCAA GTCCAATCTA TGACATCAAT TATTATACAT
 CGGAGCCCTG CCAAAAAATC AATGTGAAGC AAATCGCAGC CCGCCTCCTG CCTCCGCTCT
 ACTCACTGGT GTTCATCTTT GGTTTTGTGG GCAACATGCT GGTCATCCTC ATCCTGATAA
 ACTGCAAAAG
 K
 CTGAAGAGCA TGACTGACAT CTACCTGCTC AACCTGGCCA TCTCTGACCT GTTTTTCCTT
 CTTACTGTCC CCTTCTGGGC TCACTATGCT GCCGCCCAGT GGGACTTTGG AAATACAATG
 TGTCAACTCT TGACAGGGCT CTATTTTATA GGCTTCTTCT CTGGAATCTT CTTCATCATC
 CTCCTGACAA TCGATAGGTA CCTGGCTGTC GTCCATGCTG TGTTTGCTTT AAAAGCCAGG
 ACGGTCACCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_079509.1
dbSNP Blast Analysis
UniGene Cluster ID
546245
3D structure mapping
NP_000570  NP_001093638  
OMIM
601373.0008

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss1686966503ExAc_Aggregated_Populations121412AF 0.999275210.00072480
ss342125133ESP_Cohort_Populations 4544GF0.997359160.00264085 1.000000000.998679580.00132042

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.001+/-0.0270000

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

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