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From SNPedia

Geno Mag Summary
(A;A) 1.5 1.4x increased risk for heart disease
(A;G) 1.3 1.3x increased risk for heart disease; slightly lower (0.8x) risk for abdominal aortic aneurysm
(G;G) 1.5 moderately lower (0.64x) risk for abdominal aortic aneurysm
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
1000 genomesrs599839
23andMe allrs599839
SNP Nexus

GWAS Ctlgrs599839
Max Magnitude1.5
? (A;A) (A;G) (G;G) 28
rs599839 is a SNP found to be associated with heart disease by the German MI (Myocardial infarction) Family Study group, over several populations. The odds ratio for the (common) risk allele, rs599839(A), is 1.29 (CI: 1.18-1.40, adjusted p=0.0006).[PMID 17634449OA-icon.png]

[PMID 18262040OA-icon.png] rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. "When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus," said Sandhu. "This is equivalent to more established genes for LDL regulation, particularly APOE."

Another study also reports an association between rs599839(A) and higher LDL levels, in over 4,000 Caucasian Europeans. In one study, the (A) allele is associated with a 6% increase in nonfasting serum LDL, and in another, with a 25% increase in fasting serum LDL.[PMID 18179892OA-icon.png]

rs599839 is also considered one of the statistically stronger associations with abdominal aortic aneurysm; each (G) allele is reported as having an odds ratio of 0.8. This appears to correlate with lower LDL and higher HDL and the lower risk for coronary artery disease compared to (A;A) individuals.[PMID 23535823OA-icon.png],[PMID 26460285]

rs646776 is a surrogate for rs599839, with linkage r2=0.88. [PMID 18979498OA-icon.png] rs599839, rs4970834 and rs17228212 associated with non-HDL

SNP rs599839
PubMedID [PMID 18179892OA-icon.png]
Condition LDL cholesterol
Risk Allele G
pValue 1.00E-007
OR 0.95
95% CI 0.93-0.97

[PMID 19380133] Significant impact of chromosomal locus 1p13.3 on serum LDL cholesterol and on angiographically characterized coronary atherosclerosis

GWAS snp
PMID [PMID 18193043]
Trait LDL cholesterol
Title Newly identified loci that influence lipid concentrations and risk of coronary artery disease
Risk Allele A
P-val 6.0000000000000003E-33
Odds Ratio 5.48 [NR] mg/dl higher

[PMID 19164808OA-icon.png] Large scale association analysis of novel genetic loci for coronary artery disease

[PMID 19487539] Large scale replication analysis of loci associated with lipid concentrations in a Japanese population

[PMID 19837406] Association of the single nucleotide polymorphism rs599839 in the vicinity of the sortilin 1 gene with LDL and triglyceride metabolism, coronary heart disease and myocardial infarction The Ludwigshafen Risk and Cardiovascular Health Study

[PMID 19955471OA-icon.png] Genetic Variants Identified in a European Genome-Wide Association Study That Were Found to Predict Incident Coronary Heart Disease in the Atherosclerosis Risk in Communities Study

GWAS snp
PMID [PMID 20442857OA-icon.png]
Trait Lipoprotein-associated phospholipase A2 activity and mass
Title Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study
Risk Allele G
P-val 3E-15
Odds Ratio 5.50 [NR] nmol/ml/min decrease

[PMID 20370913OA-icon.png] Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data

[PMID 20694560] Common genetic polymorphisms in Moyamoya and atherosclerotic disease in Europeans

[PMID 21463265OA-icon.png] Association of SNP rs17465637 on Chromosome 1q41 and rs599839 on 1p13.3 with Myocardial Infarction in an American Caucasian Population

GWAS snp
PMID [PMID 21378990OA-icon.png]
Title Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease
Risk Allele A
P-val 3E-10
Odds Ratio 1.1100 [1.08-1.15]
GWAS snp
PMID [PMID 21909109]
Title Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
Risk Allele G
P-val 2E-19
Odds Ratio 5.2254 [4.09-6.37] mg/dL decrease

[PMID 22537824OA-icon.png] Smoking interacts with HLA-DRB1 shared epitope in the development of ACPA-positive rheumatoid arthritis: results from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA).

[PMID 18193044OA-icon.png] Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

[PMID 18462017OA-icon.png] Mapping the genetic architecture of gene expression in human liver.

[PMID 18649068] The novel genetic variant predisposing to coronary artery disease in the region of the PSRC1 and CELSR2 genes on chromosome 1 associates with serum cholesterol.

[PMID 18852197OA-icon.png] Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants.

[PMID 19065533] [Association of single nucleotide polymorphism rs599839 on chromosome 1p13.3 with premature coronary heart disease in a Chinese Han population].

[PMID 19161620OA-icon.png] An open access database of genome-wide association results.

[PMID 19656773OA-icon.png] A polygenic basis for four classical Fredrickson hyperlipoproteinemia phenotypes that are characterized by hypertriglyceridemia.

[PMID 19660754] Genetic variation at chromosome 1p13.3 affects sortilin mRNA expression, cellular LDL-uptake and serum LDL levels which translates to the risk of coronary artery disease.

[PMID 19679263OA-icon.png] Using new tools to define the genetic underpinnings of risky traits associated with coronary artery disease: the SardiNIA study.

[PMID 19750184OA-icon.png] Genome-wide association studies for atherosclerotic vascular disease and its risk factors.

[PMID 19802338OA-icon.png] Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication.

[PMID 19913121OA-icon.png] Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

[PMID 19924713OA-icon.png] Use of longitudinal data in genetic studies in the genome-wide association studies era: summary of Group 14.

[PMID 19951432OA-icon.png] Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease.

[PMID 20017982OA-icon.png] Genome-wide association analysis of cardiovascular-related quantitative traits in the Framingham Heart Study.

[PMID 20017983OA-icon.png] Evaluation of population impact of candidate polymorphisms for coronary heart disease in the Framingham Heart Study Offspring Cohort.

[PMID 20018038OA-icon.png] Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study.

[PMID 20098575OA-icon.png] Genetics and cardiovascular disease: Design and development of a DNA biobank.

[PMID 21804106OA-icon.png] Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration.

[PMID 21984477] Genomic risk variants at 1p13.3, 1q41, and 3q22.3 are associated with subsequent cardiovascular outcomes in healthy controls and in established coronary artery disease.

[PMID 22380622OA-icon.png] The lp13.3 genomic region -rs599839- is associated with endothelial dysfunction in patients with rheumatoid arthritis.

[PMID 22962622OA-icon.png] Early Vascular Alterations in SLE and RA Patients—A Step towards Understanding the Associated Cardiovascular Risk

GET Evidence
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.650794

[PMID 23364394] A genome-wide association study of a coronary artery disease risk variant

[PMID 23535823OA-icon.png] A sequence variant associated with Sortilin-1 (SORT1) on 1p13.3 is independently associated with Abdominal Aortic Aneurysm

[PMID 24622110OA-icon.png] Multi-Ancestral Analysis of Inflammation-Related Genetic Variants and C-Reactive Protein in the Population Architecture using Genomics and Epidemiology (PAGE) Study

[PMID 23404648OA-icon.png] An association study between genetic polymorphisms related to lipoprotein-associated phospholipase A(2) and coronary heart disease.

GWAS snp
PMID [PMID 24262325OA-icon.png]
Trait Coronary artery disease or ischemic stroke
Title Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
Risk Allele
P-val 1E-8
Odds Ratio NR NR

[PMID 24251769] LDL-c-linked SNPs are associated with LDL-c and myocardial infarction despite lipid-lowering therapy in patients with established vascular disease

[PMID 26405538OA-icon.png] Association of FURIN and ZPR1 polymorphisms with metabolic syndrome

[PMID 26464717OA-icon.png] Association of variants in CELSR2-PSRC1-SORT1 with risk of serum lipid traits, coronary artery disease and ischemic stroke