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The Major "C" allele is associated with:

Alzheimer's Disease

CC = Bad version = contributes to APOE4 when combined with CC or CT genotype for rs429358.

  • rs429358 (C;C) + rs7412 (C;C) = APOE4/APOE4 (Bad) = 12x for late-onset Alzheimer's and 61x for early-onset disease [R].

  • rs429358 (C;T) + rs7412 (C;C) = APOE4/APOE3 (Bad) = >3x increased risk for Alzheimer's; 1.4x increased risk for heart disease  [R].

  • rs429358 (T;T) + rs7412 (C;C) = APOE3/APOE3 (Good)

  • If the allele of this SNP is "C" and the same chromosome also harbors the rs429358 "C" allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease.

  • Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for rs429358 (C;C) and rs7412 (C;C) individuals, compared to the more common rs429358 (T;T) and rs7412 (C;C) (ApoE3/ApoE3) homozygotes, to be 12x for late-onset Alzheimer's and 61x for early-onset disease [R]. 

  • Meta-analyses have also supported the association between the APOE-ε4 allele and somewhat increased risk for heart disease, with an odds ratio of 1.42 (CI: 1.26 - 1.61) [R].

 

The Minor "T" allele is associated with:

Decreased Alzheimer's risk.

  • When rs7412 and rs429358 are both T (for the two SNPs located on the same chromosome) this is known as the APOE2 allele. APOE2 indicates a reduced risk of Alzheimer's disease.

rs7412

Parent Gene: APOE
Importance: 5
Minor Allele: T = 8%
Major Allele: C = 92%
My Genotype: Log In
Risk Allele: C, T, T, T, T, T, T, T, T, T

Disease/Trait: Lipid Measurement

rs7412 is associated with Lipid Measurement(R). It is reported to have a 0.75 unit decrease on Lipid metabolism phenotypes (L-LDL-FC). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Beta coefficient: 0.75 unit decrease
Risk Allele: None (P=3.00*10-58)
Context: missense_variant
Study title: Genome-wide association study identifies multiple loci influencing human serum metabolite levels. (R)
Initial sample size: 8,330 European ancestry individuals
Replication sample size:
Journal: Nat Genet (R)
Year published: Jan. 29, 2012
Strength of evidence: Strong

Disease/Trait: Ldl Cholesterol Change Measurement

rs7412 is associated with Ldl Cholesterol Change Measurement. It is reported to have a 6.2 mg/dL decrease on Response to statins (LDL cholesterol change) (baseline LDL-C). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Beta coefficient: 6.2 mg/dL decrease
Risk Allele: None (P=2.00*10-47)
Context: missense_variant
Study title: Genetic determinants of statin-induced low-density lipoprotein cholesterol reduction: the Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER) trial. (R)
Initial sample size: 6,989 European ancestry individuals
Replication sample size:
Journal: Circ Cardiovasc Genet (R)
Year published: Feb. 13, 2012
Strength of evidence: Strong

Disease/Trait: Response To Statin

rs7412 is associated with Response To Statin(R). It is reported to have a 6.2 mg/dL decrease on Response to statins (LDL cholesterol change) (baseline LDL-C). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Beta coefficient: 6.2 mg/dL decrease
Risk Allele: None (P=2.00*10-47)
Context: missense_variant
Study title: Genetic determinants of statin-induced low-density lipoprotein cholesterol reduction: the Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER) trial. (R)
Initial sample size: 6,989 European ancestry individuals
Replication sample size:
Journal: Circ Cardiovasc Genet (R)
Year published: Feb. 13, 2012
Strength of evidence: Strong

Disease/Trait: Low Density Lipoprotein Cholesterol Measurement

rs7412 is associated with Low Density Lipoprotein Cholesterol Measurement(R). It is reported to have a 12.3 mg/dL decrease on LDL cholesterol. No specific risk allele was identified in the study.

Reported risk allele frequency: 10.00%
Reported genes: APOE
Beta coefficient: 12.3 mg/dL decrease
Risk Allele: None (P=2.00*10-9)
Context: missense_variant
Study title: High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE. (R)
Initial sample size: 1,249 African American individuals
Replication sample size:
Journal: Clin Transl Sci (R)
Year published: Aug. 23, 2012
Strength of evidence: Strong

Disease/Trait: Total Cholesterol Measurement

Reported risk allele frequency: 93.00%
Reported genes: APOE
Beta coefficient: 0.413 s.d. increase
Risk Allele: C (P=8.00*10-239)
Context: missense_variant
Study title: The impact of low-frequency and rare variants on lipid levels. (R)
Initial sample size: up to 62,166 European ancestry individuals
Replication sample size:
Journal: Nat Genet (R)
Year published: May 11, 2015
Strength of evidence: Strong

Disease/Trait: Low Density Lipoprotein Cholesterol Measurement

Reported risk allele frequency: 12.00%
Reported genes: APOE
Beta coefficient: 0.48 unit decrease
Risk Allele: T (P=3.00*10-53)
Context: missense_variant
Study title: Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. (R)
Initial sample size: 1,782 Filipino ancestry mothers
Replication sample size: 1,719 Filipino ancestry offsprings
Journal: J Lipid Res (R)
Year published: Sept. 10, 2013
Strength of evidence: Strong

Disease/Trait: Total Cholesterol Measurement

Reported risk allele frequency: 12.00%
Reported genes: APOE
Beta coefficient: 0.09 unit decrease
Risk Allele: T (P=2.00*10-30)
Context: missense_variant
Study title: Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. (R)
Initial sample size: 1,782 Filipino ancestry mothers
Replication sample size: 1,719 Filipino ancestry offsprings
Journal: J Lipid Res (R)
Year published: Sept. 10, 2013
Strength of evidence: Strong

Disease/Trait: Clinical And Behavioural Ideal Cardiovascular Health

rs7412 is reported to be associated with Clinical And Behavioural Ideal Cardiovascular Health

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=9.00*10-16)
Context: missense_variant
Study title: Genetic loci associated with ideal cardiovascular health: A meta-analysis of genome-wide association studies. (R)
Initial sample size: 883 European ancestry individuals with clinical and behavioral ideal cardiovascular health, 10,825 European ancestry individuals without clinical and behavioral ideal cardiovascular health
Replication sample size: 522 European ancestry individuals
Journal: Am Heart J (R)
Year published: Jan. 23, 2016
Strength of evidence: Strong

Disease/Trait: High Density Lipoprotein Cholesterol Measurement

Reported risk allele frequency: 7.79%
Reported genes: APOE
Beta coefficient: 0.1564597 mg/dl increase
Risk Allele: T (P=6.00*10-14)
Context: missense_variant
Study title: Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants. (R)
Initial sample size: 19,223 British ancestry individuals from 6863 families.
Replication sample size:
Journal: Genome Med (R)
Year published: March 7, 2017
Strength of evidence: Strong

Disease/Trait: Total Cholesterol Measurement

Reported risk allele frequency: 7.79%
Reported genes: APOE
Beta coefficient: 0.41957754 mg/dl decrease
Risk Allele: T (P=5.00*10-94)
Context: missense_variant
Study title: Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants. (R)
Initial sample size: 19,259 British ancestry individuals from 6863 families.
Replication sample size:
Journal: Genome Med (R)
Year published: March 7, 2017
Strength of evidence: Strong

Disease/Trait: Ldl Cholesterol Change Measurement

Reported risk allele frequency: None
Reported genes: APOE
Beta coefficient: 0.313 mmol/L decrease
Risk Allele: T (P=7.00*10-15)
Context: missense_variant
Study title: Susceptibility loci for metabolic syndrome and metabolic components identified in Han Chinese: a multi-stage genome-wide association study. (R)
Initial sample size: 862 Han Chinese ancestry cases, 880 Han Chinese ancestry controls
Replication sample size: 656 Han Chinese ancestry cases, 933 Han Chinese ancestry controls
Journal: J Cell Mol Med (R)
Year published: March 30, 2017
Strength of evidence: Strong

Disease/Trait: Pulse Pressure Measurement

Reported risk allele frequency: 7.84%
Reported genes: APOE
Beta coefficient: 0.3826 unit decrease
Risk Allele: T (P=4.00*10-10)
Context: missense_variant
Study title: Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk. (R)
Initial sample size: 140,886 European ancestry individuals
Replication sample size: 190,318 European ancestry individuals
Journal: Nat Genet (R)
Year published: Jan. 30, 2017
Strength of evidence: Strong