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Reference SNP (refSNP) Cluster Report: rs1800407                 ** 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:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:A:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:T=0.0447/5295 (ExAC)
T=0.0254/127 (1000 Genomes)
T=0.0556/723 (GO-ESP)
T=0.0483/6069 (TOPMED)
HGVS Names
  • CM000677.2:g.27985172C>T
  • NC_000015.10:g.27985172C>T
  • NC_000015.9:g.28230318C>T
  • NG_009846.1:g.119141G>A
  • NM_000275.2:c.1256G>A
  • NM_001300984.1:c.1184G>A
  • NP_000266.2:p.Arg419Gln
  • NP_001287913.1:p.Arg395Gln
  • NT_187660.1:g.119439C>T
  • NW_011332701.1:g.119439C>T
  • XP_005268316.1:p.Arg395Gln
  • XP_011519942.1:p.Arg419Gln
  • XP_016877744.1:p.Arg427Gln
  • XP_016877745.1:p.Arg427Gln
  • XP_016877746.1:p.Arg403Gln
  • XP_016877747.1:p.Arg427Gln
  • XP_016877748.1:p.Arg403Gln
  • XP_016877749.1:p.Arg381Gln
  • XP_016877750.1:p.Arg362Gln
  • XP_016877751.1:p.Arg427Gln
  • XP_016877752.1:p.Arg427Gln
  • XP_016877753.1:p.Arg427Gln
  • XP_016877754.1:p.Arg427Gln
  • XR_001751294.1:n.1369G>A
Links , Linkout
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 ss48429571 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1800407 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
ss2420492HGBASE|SNP000003139fwd/TA/Gtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatc11/07/0010/10/0389Genomicunknown
ss48296094SNP500CANCER|OCA2-07byFreqfwd/TA/Ggtgtgtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatcatgct08/19/0511/03/06126Genomicunknown
ss48429571APPLERA_GI|hCV8866200byFreqrev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac09/28/0511/03/06126Genomicunknown
ss69171462PERLEGEN|PGP04770449byFreqrev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac01/30/0708/14/07127Genomicunknown
ss74814245AFFY|SNP_M-305057fwd/TA/Ggtgtgtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatcatgct08/09/0708/09/07128Genomicunknown
ss74905641ILLUMINA|ILMN_Human_1M_rs1800407fwd/TA/Ggtgtgtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatcatgct08/28/0708/29/07129Genomicunknown
ss119403922KRIBB_YJKIM|KHS1566169fwd/TA/Ggtgtgtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatcatgct02/04/0902/04/09131Genomicunknown
ss160462820ILLUMINA|HumanOmni1-Quad_v1-0_B_rs1800407-128_B_R_1513930074rev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac08/04/0910/02/09131Genomicunknown
ss172924695ILLUMINA|Human1M-Duov3_B_rs1800407-127_B_R_1513930074rev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac10/01/0910/02/09132Genomicunknown
ss207291824BCM-HGSC-SUB|BCM_CMT_1011-2730116rev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac03/15/1003/18/10132Genomicunknown
ss2367224441000GENOMES|pilot_1_CEU_6327073_chr15_25903913rev/C/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac05/01/1005/01/10132Genomicunknown
ss275517646OMIM-CURATED-RECORDS|16991fwd/TA/Ggtgtgtgtggccaggcataccggctctcccgggacgggtgtgggccatgatcatcatgct12/03/1012/03/10133Genomicunknown
ss342398390NHLBI-ESP|ESP2500-chr15-28230318byFreqrev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac03/25/1109/05/14134Genomicunknown
ss480300415ILLUMINA|HumanOmni2.5-4v1_B_rs1800407-128_B_R_1615265100rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca01/30/1210/28/16137Genomicunknown
ss480311518ILLUMINA|HumanOmniExpress-12v1_C_rs1800407-131_B_R_1862787483rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca01/30/1210/27/16137Genomicunknown
ss481067070ILLUMINA|HumanOmni1-Quad_v1-0_C_rs1800407-131_B_R_1865729798rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca01/30/1208/28/15146Genomicunknown
ss484948020ILLUMINA|HumanOmni2.5-4v1_D_rs1800407-131_B_R_1862787483rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca01/30/1210/27/16137Genomicunknown
ss4910783761000GENOMES|20110521_exome_586174_chr15_28230318rev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac02/10/1202/22/12137Genomicunknown
ss491491333EXOME_CHIP|nonsyn_207559_chr_15_28230318rev/BC/Tagcatgatgatcatggcccacacccgtcccgggagagccggtatgcctggccacacacac03/05/1203/05/12137Genomicunknown
ss491696432CLINSEQ_SNP|SNV-chr15-25903913byFreqrev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/06/1209/05/14137Genomicunknown
ss536287425ILLUMINA|HumanOmni5-4v1_B_kgp84752-0_T_R_1806830988rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca06/22/1208/29/15146Genomicunknown
ss536992291ILLUMINA|HumanOmni5-4v1_B_rs1800407-131_B_R_1894887864rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca06/22/1208/29/15146Genomicunknown
ss778697557ILLUMINA|HumanOmni25Exome-8v1_A_rs1800407-131_B_R_1867791333rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/30/1307/10/15142Genomicunknown
ss780706103ILLUMINA|HumanOmni25Exome-8v1_A_exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/30/1307/10/15146Genomicunknown
ss782920318ILLUMINA|HumanOmni2.5-4v1_H_rs1800407-131_B_R_1862787483rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/30/1307/29/15142Genomicunknown
ss783380667ILLUMINA|HumanOmniExpressExome-8v1_A_exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/31/1306/18/15146Genomicunknown
ss783883353ILLUMINA|HumanOmniExpressExome-8v1_A_rs1800407-131_B_R_1894887864rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/31/1306/18/15142Genomicunknown
ss832175442ILLUMINA|HumanOmniExpress-12v1_H_rs1800407-131_B_R_1862787483rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca09/17/1306/18/15144Genomicunknown
ss834156412ILLUMINA|HumanOmni2.5-8v1_A_rs1800407-131_B_R_1867791333rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca09/18/1307/29/15142Genomicunknown
ss991623835EVA-GONL|EVA-GONL_rs1800407rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca04/23/1404/30/14142Genomicunknown
ss1067550298JMKIDD_LAB|HGDP_exomes_chr15_28230318rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca07/09/1407/09/14142Genomicunknown
ss13528190321000GENOMES|PHASE3_V1_66123221rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca08/16/1408/16/14142Genomicunknown
ss1397692491HAMMER_LAB|HAMMER_LAB_rs1800407rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca09/30/1409/30/14146Genomicunknown
ss1584092706EVA_FINRISK|EVA_FINRISK_rs1800407rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca02/27/1502/27/15144Genomicunknown
ss1632670080EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_15_28230318_36574040rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/04/1503/04/15144Genomicunknown
ss1675664113EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_15_28230318_36574040rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/04/1503/04/15144Genomicunknown
ss1691717126EVA_EXAC|EVA_EXAC_7011237rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/04/1503/04/15144Genomicunknown
ss1695635397EVA_DECODE|EVA_DECODE_15_25903913_49970_rs1800407rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/02/1503/04/15144Genomicunknown
ss1711390080EVA_MGP|EVA_XIMO_505840rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/09/1503/09/15144Genomicunknown
ss1713477598EVA_SVP|EVA_SVP_1171965rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca03/12/1503/12/15144Genomicunknown
ss1752154412ILLUMINA|OmniExpressExome-8v1-1_B_exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/27/1506/09/15146Genomicunknown
ss1752154413ILLUMINA|OmniExpressExome-8v1-1_B_rs1800407-131_B_R_1894887864rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/27/1506/09/15146Genomicunknown
ss1917893684ILLUMINA|HumanExome-12v1-1_B_exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca10/16/1510/16/15147Genomicunknown
ss1935020885WEILL_CORNELL_DGM|SNV:chr15:28230318rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca10/16/1510/17/15147Genomicunknown
ss1946388468ILLUMINA|HumanCoreExome-12v1-0_C_exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca10/29/1510/29/15147Genomicunknown
ss1959597426ILLUMINA|exm1143095-0_T_R_1922834612rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca11/13/1511/13/15147Genomicunknown
ss2028290773JJLAB|SNP8793328rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca08/29/1608/31/16149Genomicunknown
ss2095057508ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs1800407-138_B_R_2258078256rev/BC/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca09/27/1609/27/16150Genomicunknown
ss2205523925HUMAN_LONGEVITY|HLI-15-27985172-C-Trev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca11/18/1611/18/16150Genomicunknown
ss2370059223TOPMED|15_28230318_C/Trev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca11/19/1611/19/16150Genomicunknown
ss2633208648ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs1800407-131_B_R_18948878rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca02/02/1702/02/17151Genomicunknown
ss2635056513ILLUMINA|Cancer_BeadChip_11459870_A_rs1800407-128_B_R_1615265100rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca02/02/1702/02/17151Genomicunknown
ss2741065893GNOMAD|exomes_rs1800407rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/17/1705/17/17151Genomicunknown
ss2749249550GNOMAD|coding_rs1800407rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/17/1705/17/17151Genomicunknown
ss2932980570GNOMAD|rs1800407rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/23/1705/23/17151Genomicunknown
ss2985035039AFFY|Axiom_PsorMich_Affx-11380522rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/24/1705/24/17151Genomicunknown
ss3013005249SWEGEN|NC_000015.9:g.28230318C>Trev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca05/30/1705/30/17151Genomicunknown
ss3021616166ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm1143095-0_T_R_1922834612rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca06/28/1706/28/17151Genomicunknown
ss3223219403TOPMED|TOPMed_freeze_5?chr15:27,985,172rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca10/01/1710/01/17151Genomicunknown
ss3351041754CSHL|rs1800407rev/C/Tgatgatcatggcccacacccgtcccgggagagccggtatgcctggccaca10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1800407|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 ACTGAGGGTC ATCACCTTGT GACAAATTAA CCATCACAGG GGCTCTGTGA AGGAAGAGGA
 TCAGAGGGGT GACAGTGCTG GCTAGGGAGG ATTTAGAATG TCTAGGAACT TCGATGGCCA
 GCACTGTCTC ATCTCGGCCC CCCTAGGACT CCGTGGGTCT ATGTCTTAAC CCATGGGGTA
 ATGTTAGTTT GGCTCCCTGT TCTTAAAGTC ACTAATGAAA GGCTGCCTCT GTTCTACGAG
 CCTGCTCACT CTGGCTTGTA CTCTCTCTGT GTGTGTGTGG CCAGGCATAC CGGCTCTCCC
 R
 GGGACGGGTG TGGGCCATGA TCATCATGCT CTGTCTCATC GCGGCCGTCC TCTCTGCCTT
 CTTGGACAAC GTCACCACCA TGCTCCTCTT CACGCCTGTG ACCATAAGGT ACGCAAAGCA
 CCTCTGCCGT GGGAGTTGCG GCCAGGTTCT GGCAGGCAGG GGCTCTGCCT GCACTGCCTG
 GCTCCAGGTT CCATTCTCAG GTGCATGAAA AGGTGGGGGC AGTTGAGCCC ACAGCTCACT
 GCATTCCAGT CCAGCTCGTG TCTGCTTTGT GTGACTGCAG TACATGCTAC AAGCAGTGGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
U19164
dbSNP Blast Analysis
UniGene Cluster ID
130937
OMIM
611409.0012
611409

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1800407 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1352819032EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.075500000.92449999
AFR 1322AF 0.001500000.99849999
AMR 694AF 0.031700000.96829998
SAS 978AF 0.026600000.97340006
ss1691717126ExAc_Aggregated_Populations121336AF 0.044117160.95588285
ss236722444pilot_1_CEU_low_coverage_panel 120AF 0.075000000.92500001
ss342398390ESP_Cohort_Populations 4550GF0.003076920.101978020.894945031.000000000.054065940.94593406
ss48296094P1 204AF0.020000000.039000000.941000040.001000000.039000000.96100003
CAUC1 62AF0.065000010.065000010.870000000.001000000.097000000.90300000
AFR1 48AF 1.00000000 1.00000000
HISP1 46AF 0.087000000.913000051.000000000.043000000.95699996
PAC1 48AF 1.00000000 1.00000000
ss48429571HapMap-CEUEuropean 224IG0.008928570.133928570.857142870.654721000.075892860.92410713
HapMap-JPTAsian 168IG 0.011904760.988095221.000000000.005952380.99404764
AGI_ASP populationmultiple 78IG 0.102564100.897435901.000000000.051282050.94871795
HAPMAP-CHD 170IG 0.011764710.988235291.000000000.005882350.99411762
HAPMAP-GIH 176IG 0.034090910.965909061.000000000.017045460.98295456
HAPMAP-LWK 180IG 0.011111110.988888861.000000000.005555560.99444443
HAPMAP-MEX 100IG 0.080000000.920000021.000000000.040000000.95999998
HAPMAP-TSI 176IG0.022727270.147727270.829545440.150222000.096590910.90340906
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss491696432CSAgilent 1138GF0.001998000.147852150.850149870.200325000.075924080.92407590
ss69171462HapMap-CEUEuropean 120IG0.016666670.100000000.883333330.150222000.066666670.93333334
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict		Additional Freq. Data
0.085+/-0.1880000ALFRED: The Allele Frequency Database

  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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