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Reference SNP (refSNP) Cluster Report: rs1799899                 ** With Uncertain significance 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
Association:NHGRI GWAS PheGenI
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 Uncertain significance allele [ClinVar]
MAF/MinorAlleleCount:A=0.0532/6456 (ExAC)
A=0.0306/153 (1000 Genomes)
A=0.0348/453 (GO-ESP)
A=0.0322/4046 (TOPMED)
HGVS Names
  • CM000665.2:g.133756968G>A
  • NC_000003.11:g.133475812G>A
  • NC_000003.12:g.133756968G>A
  • NG_013080.1:g.15836G>A
  • NG_013080.2:g.99971G>A
  • NM_001063.3:c.829G>A
  • NM_001354703.1:c.697G>A
  • NM_001354704.1:c.448G>A
  • NP_001054.1:p.Gly277Ser
  • NP_001341632.1:p.Gly233Ser
  • NP_001341633.1:p.Gly150Ser
  • XP_005247787.1:p.Gly150Ser
  • XP_016862578.1:p.Gly277Ser
  • XP_016862579.1:p.Gly277Ser
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 ss76888032 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1799899 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
ss2419942HGBASE|SNP000002339fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct11/07/0010/10/0389Genomicunknown
ss8820467PGA-UW-FHCRC|TF-012985byFreqfwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca06/05/0310/25/06119Genomicunknown
ss24796201SEQUENOM|sqnm138543byFreqfwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct06/18/0408/05/04123cDNAunknown
ss52975081RSG_UW|TF-010804byFreqfwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca06/06/0612/16/06127Genomicunknown
ss68875855PERLEGEN|PGP04315730byFreqfwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca01/30/0708/14/07127Genomicunknown
ss74812391AFFY|SNP_M-287665fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca08/09/0708/09/07128Genomicunknown
ss74893121ILLUMINA|ILMN_Human_1M_rs1799899fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca08/28/0708/29/07129Genomicunknown
ss76888032SI_EXO|NT_005612.15_39970958byFreqfwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca09/20/0709/05/14129Genomicunknown
ss160462701ILLUMINA|HumanOmni1-Quad_v1-0_B_rs1799899-128_B_R_1513892770rev/BC/Ttgagaagctcccagatcaagtcctccttgcgcccatacttcgggccacgacggtatgaga08/04/0910/02/09131Genomicunknown
ss162623987COMPLETE_GENOMICS|NA07022_36_chr3_134958502fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca09/28/0909/29/09132Genomicunknown
ss172924214ILLUMINA|Human1M-Duov3_B_rs1799899-128_B_R_1513892770rev/BC/Ttgagaagctcccagatcaagtcctccttgcgcccatacttcgggccacgacggtatgaga10/01/0910/02/09132Genomicunknown
ss2320400521000GENOMES|pilot_1_CEU_1644681_chr3_134958502fwd/A/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca05/01/1005/01/10132Genomicunknown
ss244238315OMICIA|2010_April_001_211_TF_190000_0008fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca05/27/1005/28/10132Genomicunknown
ss244284956ILLUMINA|CVDSNP55v1_A_rs1799899rev/BC/Ttgagaagctcccagatcaagtcctccttgcgcccatacttcgggccacgacggtatgaga06/10/1006/10/10132Genomicunknown
ss275518585OMIM-CURATED-RECORDS|5664fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca12/08/1012/08/10133Genomicunknown
ss342147896NHLBI-ESP|ESP2500-chr3-133475812byFreqfwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca03/25/1109/05/14134Genomicunknown
ss480300083ILLUMINA|HumanOmni2.5-4v1_B_rs1799899-128_B_R_1690722058fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct01/30/1210/28/16137Genomicunknown
ss480311172ILLUMINA|HumanOmniExpress-12v1_C_rs1799899-131_B_R_1857012294fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct01/30/1210/27/16137Genomicunknown
ss481066599ILLUMINA|HumanOmni1-Quad_v1-0_C_rs1799899-131_B_R_1865343902fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct01/30/1208/28/15146Genomicunknown
ss484947852ILLUMINA|HumanOmni2.5-4v1_D_rs1799899-131_B_R_1857012294fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct01/30/1210/28/16137Genomicunknown
ss4908743531000GENOMES|20110521_exome_382151_chr3_133475812fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca02/10/1202/21/12137Genomicunknown
ss491346665EXOME_CHIP|nonsyn_62892_chr_3_133475812fwd/TA/Gtctcataccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagcttctca03/05/1203/05/12137Genomicunknown
ss491842760CLINSEQ_SNP|SNV-chr3-134958502byFreqfwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/06/1209/05/14137Genomicunknown
ss536992195ILLUMINA|HumanOmni5-4v1_B_rs1799899-131_B_R_1894880482fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct06/22/1208/28/15146Genomicunknown
ss778841462ILLUMINA|HumanOmni25Exome-8v1_A_rs1799899-131_B_R_1867764235fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/30/1307/09/15146Genomicunknown
ss780822291ILLUMINA|HumanOmni25Exome-8v1_A_exm352193-0_T_F_1922147285fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/30/1307/09/15146Genomicunknown
ss782920234ILLUMINA|HumanOmni2.5-4v1_H_rs1799899-131_B_R_1857012294fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/30/1307/28/15146Genomicunknown
ss783504779ILLUMINA|HumanOmniExpressExome-8v1_A_exm352193-0_T_F_1922147285fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/31/1306/19/15146Genomicunknown
ss783883277ILLUMINA|HumanOmniExpressExome-8v1_A_rs1799899-131_B_R_1894880482fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/31/1306/19/15146Genomicunknown
ss832175356ILLUMINA|HumanOmniExpress-12v1_H_rs1799899-131_B_R_1857012294fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct09/17/1306/18/15146Genomicunknown
ss834302019ILLUMINA|HumanOmni2.5-8v1_A_rs1799899-131_B_R_1867764235fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct09/18/1307/28/15146Genomicunknown
ss979181912EVA-GONL|EVA-GONL_rs1799899fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct04/23/1404/24/14142Genomicunknown
ss1067455533JMKIDD_LAB|HGDP_exomes_chr3_133475812fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct07/09/1407/09/14142Genomicunknown
ss1070845935JMKIDD_LAB|HGDP_WGS_chr3_133475812fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct07/10/1407/10/14142Genomicunknown
ss13062333171000GENOMES|PHASE3_V1_17588121fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct08/16/1408/16/14142Genomicunknown
ss1397352225HAMMER_LAB|HAMMER_LAB_rs1799899fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct09/30/1409/30/14146Genomicunknown
ss1580190168EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1799899fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct02/19/1502/20/15144Genomicunknown
ss1584030594EVA_FINRISK|EVA_FINRISK_rs1799899fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct02/27/1502/27/15144Genomicunknown
ss1588667366EVA_DECODE|EVA_DECODE_3_134958502_1045008_rs1799899fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/02/1503/03/15144Genomicunknown
ss1608253440EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_133475812_9745463fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/04/1503/04/15144Genomicunknown
ss1651247473EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_133475812_9745463fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/04/1503/04/15144Genomicunknown
ss1687220696EVA_EXAC|EVA_EXAC_2157162fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/04/1503/04/15144Genomicunknown
ss1711035462EVA_MGP|EVA_XIMO_151222fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/09/1503/09/15144Genomicunknown
ss1712613814EVA_SVP|EVA_SVP_308248fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct03/12/1503/12/15144Genomicunknown
ss1752440692ILLUMINA|OmniExpressExome-8v1-1_B_rs1799899-131_B_R_2087475830fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/27/1506/09/15146Genomicunknown
ss1917773090ILLUMINA|HumanExome-12v1-1_B_exm352193-0_T_F_1922147285fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct10/16/1510/16/15147Genomicunknown
ss1922409128WEILL_CORNELL_DGM|SNV:chr3:133475812fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct10/16/1510/17/15147Genomicunknown
ss1946096651ILLUMINA|HumanCoreExome-12v1-0_C_exm352193-0_T_F_2065688584fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct10/29/1510/29/15147Genomicunknown
ss1958607394ILLUMINA|exm352193-0_T_F_1922147285fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct11/13/1511/13/15147Genomicunknown
ss2021773206JJLAB|SNP2275761fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct08/29/1608/30/16149Genomicunknown
ss2095138077ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs1799899-138_B_R_2264357641fwd/TA/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct09/27/1609/27/16150Genomicunknown
ss2149867806USC_VALOUEV|NC_000003.11:g.133475812G>Afwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct11/17/1611/17/16150Genomicunknown
ss2255973616HUMAN_LONGEVITY|HLI-3-133756968-G-Afwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct11/18/1611/18/16150Genomicunknown
ss2423347333TOPMED|3_133475812_G/Afwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct11/19/1611/19/16150Genomicunknown
ss2634014572ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_Seq-rs1799899-131_B_R_2130fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct02/02/1702/02/17151Genomicunknown
ss2634014573ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs1799899-131_B_R_20874758fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct02/02/1702/02/17151Genomicunknown
ss2734086482GNOMAD|exomes_rs1799899fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/17/1705/17/17151Genomicunknown
ss2747106532GNOMAD|coding_rs1799899fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/17/1705/17/17151Genomicunknown
ss2799340143GNOMAD|rs1799899fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/18/1705/18/17151Genomicunknown
ss2985270733AFFY|Axiom_PsorMich_Affx-21200849fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/24/1705/24/17151Genomicunknown
ss2985894717AFFY|Axiom_Smokesc1_Affx-21200849fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/24/1705/24/17151Genomicunknown
ss2993229737SWEGEN|NC_000003.11:g.133475812G>Afwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct05/30/1705/30/17151Genomicunknown
ss3022288622ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm352193-0_T_F_1922147285fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct06/28/1706/28/17151Genomicunknown
ss3024653368BIOINF_KMB_FNS_UNIBA|3.133756968G>Afwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct07/05/1707/05/17151Genomicunknown
ss3345276352CSHL|rs1799899fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct10/02/1710/02/17151Genomicunknown
ss3406011161TOPMED|TOPMed_freeze_5?chr3:133,756,968fwd/A/Gtaccgtcgtggcccgaagtatgggcgcaaggaggacttgatctgggagct10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1799899|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 GTTGCCATAA CCAAAGACTG GGGGTTGGTG CTGCTAAGAT CAGGCTCATG GTGGAATGAG
 GAGCAATCAC TGCTACATGG GCATCAGAAG CCTTTACCTG GCTGTGGGCT CTTGAGCGAG
 TCATTCTCCC GCATGTTCTC TGGCCTTCAG TGCTCACTCC AGACCTCTCA GCTCATACTT
 TCTATGATCA ATTGAATTTC AAGGATGGGC ACCACAGCCC ATGGCTCTCC TGTGTTAAGC
 TCACCTGGGC TTTCCCTCCC CAGAGAACTT GGCAAACAAG GCTGACAGGG ACCAGTATGA
 GCTGCTTTGC CTGGACAACA CCCGGAAGCC GGTAGATGAA TACAAGGACT GCCACTTGGC
 CCAGGTCCCT TCTCATACCG TCGTGGCCCG AAGTATGGGC
 R
 GCAAGGAGGA CTTGATCTGG GAGCTTCTCA ACCAGGCCCA GGTATCCCCA CCTGCCATCC
 TCCCCTCCAG CTTAGTGCTC CCTGCTTGGA TTTGGGGGTT TTCCTCCTGG CCATCTTGTC
 ACTCTGGAAG TCTGTGTGTT CAGGATACAG TGGGAGCCAT GCCACATGTC ACTAAGTTCT
 CTAAAAGCTG GGACTCCCCA CAGAGCAGCA GGGAGCCTGC TGTGGTGCTA CCGTCTGCCG
 CCCTTGCCTT TCTGGCTGGT GACACCTGAA GAGGCTCTGT ATTGCTCTGT TGCATTCCTT
 TCTACCTAAA CTTCAAGGCC CAAAGCTAAA CCCCTCCCCA AGGAGGCTTT CCATGACCCT
 CCCAGAAGGA AATGGTCTCT CTCCCCATGC CCCTCAGCCC

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm138543 NT_005612.15
dbSNP Blast Analysis
UniGene Cluster ID
518267
3D structure mapping
NP_001054  
OMIM
190000.0008

  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
ss1306233317EAS 1008AF 1.00000000
EUR 1006AF 0.070600000.92939997
AFR 1322AF 0.001500000.99849999
AMR 694AF 0.038900000.96110004
SAS 978AF 0.054200000.94579995
ss162623987CEUEuropean 2IG1.00000000 1.00000000
ss1687220696ExAc_Aggregated_Populations121412AF 0.053174320.94682568
ss232040052pilot_1_CEU_low_coverage_panel 120AF 0.050000000.94999999
ss24796201CEPH 184AF 0.040000000.95999998
ss342147896ESP_Cohort_Populations 4552GF0.001318100.053163450.945518430.342782000.027899820.97210020
ss491842760CSAgilent 1323GF 0.101000000.898999990.751830000.050500000.94950002
ss52975081MCL_HISP-PANEL 90IG 0.044444450.955555561.000000000.022222220.97777778
MCL_AD-PANEL 46IG 1.00000000 1.00000000
MCL_ASIAN-PANEL 92IG 1.00000000 1.00000000
MCL_CEPH-PANEL 88IG0.022727270.068181820.909090940.020022000.056818180.94318181
MCL_YORUB-PANEL 46IG 1.00000000 1.00000000
ss76888032HapMap-CEUEuropean 226IG0.008849560.061946900.929203510.050043000.039823010.96017700
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-GIH 176IG 0.102272730.897727251.000000000.051136360.94886363
HAPMAP-LWK 180IG 0.011111110.988888861.000000000.005555560.99444443
HAPMAP-MEX 100IG 0.080000000.920000021.000000000.040000000.95999998
HAPMAP-MKK 286IG 0.034965030.965034961.000000000.017482520.98251748
HAPMAP-TSI 176IG0.011363640.170454550.818181811.000000000.096590910.90340906
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss8820467PGA-AFRICAN-PANELAfrican American 48IG 1.00000000 1.00000000
PGA-EUROPEAN-PANELEuropean 46IG 0.086956520.913043501.000000000.043478260.95652175

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.101+/-0.2010000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNYES

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