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The C (minor) allele is associated with:

C = Bad version = predictive of APOE4

  • 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 rs7412 "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 homozygous rs429358(C;C) individuals compared to the more common 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].

rs429358

Parent Gene: APOE
Importance: 5
Minor Allele: C = 15%
Major Allele: T = 85%
My Genotype: Log In
Risk Allele: T, C, C, C, C, C, T

Disease/Trait: High Density Lipoprotein Cholesterol Measurement

The T allele of rs429358 is reported to be associated with High Density Lipoprotein Cholesterol Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with HDL cholesterol.

Reported risk allele frequency: 84.00%
Reported genes: APOE
Beta coefficient: 0.066 s.d. increase
Risk Allele: T (P=1.00*10-14)
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: Lewy Body Dementia Measurement

The C allele of rs429358 is reported to be associated with Lewy Body Dementia Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Ordinal I).

Reported risk allele frequency: 73.20%
Reported genes: APOE
Beta coefficient: 0.4997 unit decrease
Risk Allele: C (P=1.00*10-12)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: Lewy Body Dementia

The C allele of rs429358 is reported to be associated with Lewy Body Dementia(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Ordinal I).

Reported risk allele frequency: 73.20%
Reported genes: APOE
Beta coefficient: 0.4997 unit decrease
Risk Allele: C (P=1.00*10-12)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: Lewy Body Dementia Measurement

The C allele of rs429358 is reported to be associated with Lewy Body Dementia Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Ordinal II).

Reported risk allele frequency: 73.47%
Reported genes: APOE
Beta coefficient: 0.508 unit decrease
Risk Allele: C (P=5.00*10-12)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: Lewy Body Dementia

The C allele of rs429358 is reported to be associated with Lewy Body Dementia(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Ordinal II).

Reported risk allele frequency: 73.47%
Reported genes: APOE
Beta coefficient: 0.508 unit decrease
Risk Allele: C (P=5.00*10-12)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: T-Tau Measurement

rs429358 is associated with T-Tau Measurement(R). It is reported to association with Alzheimer's disease biomarkers (AB1-42, p-tau181p, p-tau181p/AB1-42, t-tau/AB1-42). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-6)
Context: missense_variant
Study title: Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort. (R)
Initial sample size: 96 European ancestry Alzheimer disease cases, 176 European ancestry individuals with mild cognitive impairment, 102 European ancestry controls
Replication sample size:
Journal: Neurology (R)
Year published: Dec. 1, 2010
Strength of evidence: Strong

Disease/Trait: Alzheimers Disease

rs429358 is associated with Alzheimers Disease. It is reported to association with Alzheimer's disease biomarkers (AB1-42, p-tau181p, p-tau181p/AB1-42, t-tau/AB1-42). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-6)
Context: missense_variant
Study title: Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort. (R)
Initial sample size: 96 European ancestry Alzheimer disease cases, 176 European ancestry individuals with mild cognitive impairment, 102 European ancestry controls
Replication sample size:
Journal: Neurology (R)
Year published: Dec. 1, 2010
Strength of evidence: Strong

Disease/Trait: Beta-Amyloid 1-42 Measurement

rs429358 is associated with Beta-Amyloid 1-42 Measurement(R). It is reported to association with Alzheimer's disease biomarkers (AB1-42, p-tau181p, p-tau181p/AB1-42, t-tau/AB1-42). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-6)
Context: missense_variant
Study title: Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort. (R)
Initial sample size: 96 European ancestry Alzheimer disease cases, 176 European ancestry individuals with mild cognitive impairment, 102 European ancestry controls
Replication sample size:
Journal: Neurology (R)
Year published: Dec. 1, 2010
Strength of evidence: Strong

Disease/Trait: P-Tau Measurement

rs429358 is associated with P-Tau Measurement(R). It is reported to association with Alzheimer's disease biomarkers (AB1-42, p-tau181p, p-tau181p/AB1-42, t-tau/AB1-42). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-6)
Context: missense_variant
Study title: Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort. (R)
Initial sample size: 96 European ancestry Alzheimer disease cases, 176 European ancestry individuals with mild cognitive impairment, 102 European ancestry controls
Replication sample size:
Journal: Neurology (R)
Year published: Dec. 1, 2010
Strength of evidence: Strong

Disease/Trait: Neuroimaging Measurement

rs429358 is associated with Neuroimaging Measurement(R). It is reported to association with Brain imaging (multiple phenotypes). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-7)
Context: missense_variant
Study title: Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. (R)
Initial sample size: 175 European ancestry Alzheimer cases, 354 European ancestry amnestic mild cognitive impairment cases, 204 European ancestry controls
Replication sample size:
Journal: Neuroimage (R)
Year published: Jan. 22, 2010
Strength of evidence: Strong

Disease/Trait: Cerebral Amyloid Deposition Measurement

The C allele of rs429358 is reported to be associated with Cerebral Amyloid Deposition Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Cerebral amyloid deposition positivity (PET imaging).

Reported risk allele frequency: 85.00%
Reported genes: APOE
Odds ratio: 4.72
Risk Allele: C (P=5.00*10-20)
Context: missense_variant
Study title: Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level. (R)
Initial sample size: up to 350 European and other ancestry positive individuals, up to 296 European and other ancestry negative individuals
Replication sample size:
Journal: PLoS One (R)
Year published: Aug. 7, 2015
Strength of evidence: Strong

Disease/Trait: Lewy Body Dementia Measurement

The C allele of rs429358 is reported to be associated with Lewy Body Dementia Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Case/control).

Reported risk allele frequency: 73.44%
Reported genes: APOE
Beta coefficient: 0.4905 unit decrease
Risk Allele: C (P=3.00*10-11)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: Lewy Body Dementia

The C allele of rs429358 is reported to be associated with Lewy Body Dementia(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Lewy body disease (Case/control).

Reported risk allele frequency: 73.44%
Reported genes: APOE
Beta coefficient: 0.4905 unit decrease
Risk Allele: C (P=3.00*10-11)
Context: missense_variant
Study title: Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias. (R)
Initial sample size: up to 3,526 individuals
Replication sample size:
Journal: PLoS Genet (R)
Year published: Sept. 4, 2014
Strength of evidence: Strong

Disease/Trait: Alzheimers Disease

The C allele of rs429358 is reported to be associated with Alzheimers Disease. Your genotype was not identified for this SNP so we are unable to comment on your association with Alzheimer's disease biomarkers (Cortical Ab).

Reported risk allele frequency: 28.00%
Reported genes: APOE
Risk Allele: C (P=5.00*10-14)
Context: missense_variant
Study title: APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study. (R)
Initial sample size: 555 European ancestry individuals
Replication sample size:
Journal: Mol Psychiatry (R)
Year published: Feb. 19, 2013
Strength of evidence: Strong

Disease/Trait: Amyloid-Beta Measurement

The C allele of rs429358 is reported to be associated with Amyloid-Beta Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Alzheimer's disease biomarkers (Cortical Ab).

Reported risk allele frequency: 28.00%
Reported genes: APOE
Risk Allele: C (P=5.00*10-14)
Context: missense_variant
Study title: APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study. (R)
Initial sample size: 555 European ancestry individuals
Replication sample size:
Journal: Mol Psychiatry (R)
Year published: Feb. 19, 2013
Strength of evidence: Strong

Disease/Trait: Alzheimers Disease

rs429358 is associated with Alzheimers Disease. It is reported to have a 0.4 unit decrease on Cerebrospinal AB1-42 levels in Alzheimer's disease dementia. No specific risk allele was identified in the study.

Reported risk allele frequency: 44.20%
Reported genes: APOE
Beta coefficient: 0.4 unit decrease
Risk Allele: None (P=4.00*10-17)
Context: missense_variant
Study title: SUCLG2 identified as both a determinator of CSF Aß1-42-levels and an attenuator of cognitive decline in Alzheimer's disease. (R)
Initial sample size: 363 European ancestry individuals
Replication sample size: 515 individuals
Journal: Hum Mol Genet (R)
Year published: July 15, 2014
Strength of evidence: Strong

Disease/Trait: Beta-Amyloid 1-42 Measurement

rs429358 is associated with Beta-Amyloid 1-42 Measurement(R). It is reported to have a 0.4 unit decrease on Cerebrospinal AB1-42 levels in Alzheimer's disease dementia. No specific risk allele was identified in the study.

Reported risk allele frequency: 44.20%
Reported genes: APOE
Beta coefficient: 0.4 unit decrease
Risk Allele: None (P=4.00*10-17)
Context: missense_variant
Study title: SUCLG2 identified as both a determinator of CSF Aß1-42-levels and an attenuator of cognitive decline in Alzheimer's disease. (R)
Initial sample size: 363 European ancestry individuals
Replication sample size: 515 individuals
Journal: Hum Mol Genet (R)
Year published: July 15, 2014
Strength of evidence: Strong

Disease/Trait: Wet Macular Degeneration

rs429358 is associated with Wet Macular Degeneration(R). It is reported to increased association with Advanced age-related macular degeneration (EA). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Odds ratio: 1.4285715
Risk Allele: None (P=2.00*10-42)
Context: missense_variant
Study title: A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. (R)
Initial sample size: 16,144 European ancestry cases, 17,832 European ancestry controls
Replication sample size: 473 Asian ancestry cases, 1,099 Asian ancestry controls, 52 African ancestry cases, 361 African ancestry cases, 254 other non-European ancestry cases, 694 other non-European ancestry controls
Journal: Nat Genet (R)
Year published: Dec. 21, 2015
Strength of evidence: Strong

Disease/Trait: Age-Related Macular Degeneration

rs429358 is associated with Age-Related Macular Degeneration(R). It is reported to increased association with Advanced age-related macular degeneration (EA). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Odds ratio: 1.4285715
Risk Allele: None (P=2.00*10-42)
Context: missense_variant
Study title: A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. (R)
Initial sample size: 16,144 European ancestry cases, 17,832 European ancestry controls
Replication sample size: 473 Asian ancestry cases, 1,099 Asian ancestry controls, 52 African ancestry cases, 361 African ancestry cases, 254 other non-European ancestry cases, 694 other non-European ancestry controls
Journal: Nat Genet (R)
Year published: Dec. 21, 2015
Strength of evidence: Strong

Disease/Trait: Atrophic Macular Degeneration

rs429358 is associated with Atrophic Macular Degeneration. It is reported to increased association with Advanced age-related macular degeneration (EA). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Odds ratio: 1.4285715
Risk Allele: None (P=2.00*10-42)
Context: missense_variant
Study title: A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. (R)
Initial sample size: 16,144 European ancestry cases, 17,832 European ancestry controls
Replication sample size: 473 Asian ancestry cases, 1,099 Asian ancestry controls, 52 African ancestry cases, 361 African ancestry cases, 254 other non-European ancestry cases, 694 other non-European ancestry controls
Journal: Nat Genet (R)
Year published: Dec. 21, 2015
Strength of evidence: Strong

Disease/Trait: Cerebral Amyloid Deposition Measurement

The T allele of rs429358 is reported to be associated with Cerebral Amyloid Deposition Measurement(R). Your genotype was not identified for this SNP so we are unable to comment on your association with Cerebral amyloid deposition (PET imaging).

Reported risk allele frequency: 2.00%
Reported genes: APOE
Beta coefficient: 0.13 unit decrease
Risk Allele: T (P=8.00*10-32)
Context: missense_variant
Study title: Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level. (R)
Initial sample size: up to 883 European and other ancestry individuals
Replication sample size:
Journal: PLoS One (R)
Year published: Aug. 7, 2015
Strength of evidence: Strong

Disease/Trait: Cognitive Decline

rs429358 is associated with Cognitive Decline(R). It is reported to have a 0.01 unit decrease on Cognitive decline (age-related). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Beta coefficient: 0.01 unit decrease
Risk Allele: None (P=2.00*10-14)
Context: missense_variant
Study title: Genetic architecture of age-related cognitive decline in African Americans. (R)
Initial sample size: 3,964 African American ancestry individuals.
Replication sample size:
Journal: Neurol Genet (R)
Year published: Dec. 21, 2016
Strength of evidence: Strong

Disease/Trait: Neuroimaging Measurement

rs429358 is associated with Neuroimaging Measurement(R). It is reported to association with Brain imaging (grey matter density of the right hippocampus). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=1.00*10-9)
Context: missense_variant
Study title: Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. (R)
Initial sample size: 175 European ancestry Alzheimer cases, 354 European ancestry amnestic mild cognitive impairment cases, 204 European ancestry controls
Replication sample size:
Journal: Neuroimage (R)
Year published: Jan. 22, 2010
Strength of evidence: Strong

Disease/Trait: Blood Protein Measurement

rs429358 is associated with Blood Protein Measurement. It is reported to association with Blood protein levels (EA, Apolipoprotein E). No specific risk allele was identified in the study.

Reported risk allele frequency: None
Reported genes: APOE
Risk Allele: None (P=2.00*10-12)
Context: missense_variant
Study title: Connecting genetic risk to disease end points through the human blood plasma proteome. (R)
Initial sample size: 997 European ancestry individuals
Replication sample size: 338 Arab, South Asian and Filipino ancestry individuals
Journal: Nat Commun (R)
Year published: Feb. 27, 2017
Strength of evidence: Strong