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Reference SNP (refSNP) Cluster Report: rs1800452                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:89/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:A:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.0050/610 (ExAC)
A=0.0120/60 (1000 Genomes)
A=0.0012/15 (GO-ESP)
A=0.0052/651 (TOPMED)
HGVS Names
  • CM000665.2:g.46373570G>A
  • NC_000003.11:g.46415061G>A
  • NC_000003.12:g.46373570G>A
  • NG_012637.1:g.8429G>A
  • NM_000579.3:c.668G>A
  • NM_001100168.1:c.668G>A
  • NP_000570.1:p.Arg223Gln
  • NP_001093638.1:p.Arg223Gln
  • NR_125406.1:n.392-2153C>T
  • XP_005264911.1:p.Arg223Gln
  • XP_005264912.1:p.Ser212=
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 ss277112191 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800452 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
ss2420544HGBASE|SNP000003200fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac11/07/0010/10/0389Genomicunknown
ss263193952OMIM-CURATED-RECORDS|10135fwd/TA/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc10/28/1010/28/10133Genomicunknown
ss277112191GMI|GMI_AK_SNP_1432400fwd/A/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc12/16/1012/16/10137Genomicunknown
ss3306655851000GENOMES|20100804_snps_2309121_chr3_46415061fwd/A/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc03/22/1103/22/11134Genomicunknown
ss342125168NHLBI-ESP|ESP2500-chr3-46415061byFreqfwd/TA/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc03/25/1109/05/14134Genomicunknown
ss4898750851000GENOMES|20110521_exome_370769_chr3_46415061fwd/TA/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc02/10/1202/21/12137Genomicunknown
ss491338711EXOME_CHIP|nonsyn_54938_chr_3_46415061fwd/TA/Ggctactcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcacagggc03/05/1203/05/12137Genomicunknown
ss534292981ILLUMINA|HumanOmni5-4v1_B_kgp17889622-0_T_F_1897509603fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac06/22/1208/28/15146Genomicunknown
ss650266537SSMP|3_46415061fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac12/14/1202/10/15138Genomicunknown
ss780815979ILLUMINA|HumanOmni25Exome-8v1_A_exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/30/1307/09/15146Genomicunknown
ss783498161ILLUMINA|HumanOmniExpressExome-8v1_A_exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/31/1306/19/15146Genomicunknown
ss978547370EVA-GONL|EVA-GONL_rs1800452fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac04/23/1404/24/14142Genomicunknown
ss1067450462JMKIDD_LAB|HGDP_exomes_chr3_46415061fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac07/09/1407/09/14142Genomicunknown
ss1070380433JMKIDD_LAB|HGDP_WGS_chr3_46415061fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac07/10/1407/10/14142Genomicunknown
ss13038235571000GENOMES|PHASE3_V1_15082174fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac08/16/1408/16/14142Genomicunknown
ss1606974203EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_46415061_8344543fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac03/04/1503/04/15144Genomicunknown
ss1649968236EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_46415061_8344543fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac03/04/1503/04/15144Genomicunknown
ss1686966622EVA_EXAC|EVA_EXAC_1884283fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac03/04/1503/04/15144Genomicunknown
ss1711015386EVA_MGP|EVA_XIMO_131925fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac03/09/1503/09/15144Genomicunknown
ss1752471725ILLUMINA|OmniExpressExome-8v1-1_B_exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/27/1506/09/15146Genomicunknown
ss1917766157ILLUMINA|HumanExome-12v1-1_B_exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac10/16/1510/16/15147Genomicunknown
ss1946081402ILLUMINA|HumanCoreExome-12v1-0_C_exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac10/29/1510/29/15147Genomicunknown
ss1958559369ILLUMINA|exm307688-0_T_F_1922223191fwd/TA/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac11/13/1511/13/15147Genomicunknown
ss2149525657USC_VALOUEV|NC_000003.11:g.46415061G>Afwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac11/17/1611/17/16150Genomicunknown
ss2251182135HUMAN_LONGEVITY|HLI-3-46373570-G-Afwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac11/18/1611/18/16150Genomicunknown
ss2418265783TOPMED|3_46415061_G/Afwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac11/19/1611/19/16150Genomicunknown
ss2625226082SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1225418fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac01/06/1701/06/17151Genomicunknown
ss2704897767GRF|rs1800452fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac02/13/1702/13/17151Genomicunknown
ss2733690727GNOMAD|exomes_rs1800452fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/17/1705/17/17151Genomicunknown
ss2746990384GNOMAD|coding_rs1800452fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/17/1705/17/17151Genomicunknown
ss2792417205GNOMAD|rs1800452fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/18/1705/18/17151Genomicunknown
ss2985254173AFFY|Axiom_PsorMich_Affx-22374921fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/24/1705/24/17151Genomicunknown
ss2992240510SWEGEN|NC_000003.11:g.46415061G>Afwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac05/30/1705/30/17151Genomicunknown
ss3022235377ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm307688-0_T_F_1922223191fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac06/28/1706/28/17151Genomicunknown
ss3389293305TOPMED|TOPMed_freeze_5?chr3:46,373,570fwd/A/Gtcgggaatcctaaaaactctgcttcgtgtcgaaatgagaagaagaggcac10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800452|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 AAACTGCAAA AGGCTGAAGA GCATGACTGA CATCTACCTG CTCAACCTGG CCATCTCTGA
 CCTGTTTTTC CTTCTTACTG TCCCCTTCTG GGCTCACTAT GCTGCCGCCC AGTGGGACTT
 TGGAAATACA ATGTGTCAAC TCTTGACAGG GCTCTATTTT ATAGGCTTCT TCTCTGGAAT
 CTTCTTCATC ATCCTCCTGA CAATCGATAG GTACCTGGCT GTCGTCCATG CTGTGTTTGC
 TTTAAAAGCC AGGACGGTCA CCTTTGGGGT GGTGACAAGT GTGATCACTT GGGTGGTGGC
 TGTGTTTGCG TCTCTCCCAG GAATCATCTT TACCAGATCT CAAAAAGAAG GTCTTCATTA
 CACCTGCAGC TCTCATTTTC CATACAGTCA GTATCAATTC TGGAAGAATT TCCAGACATT
 AAAGATAGTC ATCTTGGGGC TGGTCCTGCC GCTGCTTGTC ATGGTCATCT GCTACTCGGG
 AATCCTAAAA ACTCTGCTTC
 R
 GTGTCGAAAT GAGAAGAAGA GGCACAGGGC TGTGAGGCTT ATCTTCACCA TCATGATTGT
 TTATTTTCTC TTCTGGGCTC CCTACAACAT TGTCCTTCTC CTGAACACCT TCCAGGAATT
 CTTTGGCCTG AATAATTGCA GTAGCTCTAA CAGGTTGGAC CAAGCTATGC AGGTGACAGA
 GACTCTTGGG ATGACGCACT GCTGCATCAA CCCCATCATC TATGCCTTTG TCGGGGAGAA
 GTTCAGAAAC TACCTCTTAG TCTTCTTCCA AAAGCACATT GCCAAACGCT TCTGCAAATG
 CTGTTCTATT TTCCAGCAAG AGGCTCCCGA GCGAGCAAGC TCAGTTTACA CCCGATCCAC
 TGGGGAGCAG GAAATATCTG TGGGCTTGTG ACACGGACTC AAGTGGGCTG GTGACCCAGT
 CAGAGTTGTG CACATGGCTT AGTTTTCATA CACAGCCTGG GCTGGGGGTG GGGTGGGAGA
 GGTCTTTTTT AAAAGGAAGT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
X91492
dbSNP Blast Analysis
UniGene Cluster ID
546245
3D structure mapping
NP_000570  NP_001093638  
OMIM
601373.0003

  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/G
G/G
HWPA
G
ss1303823557EAS 1008AF 0.056500000.94349998
EUR 1006AF 0.001000000.99900001
AFR 1322AF 1.00000000
AMR 694AF 1.00000000
SAS 978AF 0.002000000.99800003
ss1686966622ExAc_Aggregated_Populations121412AF 0.005024220.99497581
ss342125168ESP_Cohort_Populations 4534GF 0.000882220.999117791.000000000.000441110.99955887

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.010+/-0.0700000

  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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