Can you give a list of SNPs that are associated with alzheimers?
Several well-established SNPs are linked to Alzheimer's disease risk. The most prominent ones include variants in APOE (especially rs429358 and rs7412 defining the ε4 allele), CLU, CR1, PICALM, BIN1, and TREM2. Here is a quick overview while I pull a more complete, up-to-date list.
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Searching PubMed
"Alzheimer's disease" AND "single nucleotide polymorphism" AND "genome-wide association"
Searching the Web
SNPs associated with Alzheimer's disease GWAS 2024 2025 complete list
Reading Article
PMID: 42237039
Reading Article
PMID: 39023044
Searching the Web
Bellenguez 2022 Nature Genetics Alzheimer GWAS SNPs list rs numbers loci
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https://hal.science/hal-03668928v1/file/BPH_NG_2022_Bellengu…
Here is a well-organized reference list of SNPs associated with Alzheimer's disease, drawn from the landmark Bellenguez et al. 2022 Nature Genetics GWAS (the largest European-ancestry AD GWAS at the time, ~111,000 cases/controls), the 2026 consensus meta-analysis (PMID: 42237039, 91 loci total), and other recent multi-ancestry studies.
SNPs Associated with Alzheimer's Disease
Tier 1 - Strongest / Most Replicated Loci
| SNP | Gene/Locus | Chr | Effect (OR) | Notes |
|---|---|---|---|---|
| rs429358 | APOE | 19 | ~3.7 (ε4 het), ~12 (ε4 hom) | Defines APOE ε4 allele; highest known genetic risk factor |
| rs7412 | APOE | 19 | ~0.6 (protective) | Defines APOE ε2 (protective) allele |
| rs6733839 | BIN1 | 2 | 1.17 | One of the most replicated non-APOE loci |
| rs75932628 | TREM2 | 6 | 2.39 | Rare missense variant (R47H); major microglial risk variant |
| rs143332484 | TREM2 | 6 | 1.41 | Second TREM2 missense variant (R62H) |
| rs3851179 | PICALM | 11 | 0.90 | Protective; involved in clathrin-mediated endocytosis |
| rs12151021 | ABCA7 | 19 | 1.10 | Lipid transport; more prominent in African ancestry |
| rs679515 | CR1 | 1 | 1.13 | Complement receptor; immune/amyloid clearance |
| rs10933431 | INPP5D | 2 | 0.93 | Microglial gene; SHIP1 phosphatase |
| rs74685827 / rs11218343 | SORL1 | 11 | 1.19 / 0.84 | APP sorting receptor; rare variants also pathogenic |
| rs17125924 | FERMT2 | 14 | 1.10 | Cell adhesion / tau-related |
| rs117618017 | APH1B | 15 | 1.11 | γ-secretase component |
Tier 2 - Well-Established Loci (Replicated in Multiple GWAS)
| SNP | Gene/Locus | Chr | Effect (OR) | Pathway |
|---|---|---|---|---|
| rs6605556 | HLA-DQA1 | 6 | 0.91 | Immune/MHC |
| rs10947943 | UNC5CL/TREM2 | 6 | 0.94 | Microglial |
| rs6014724 | CASS4 | 20 | 0.89 | Tau scaffold |
| rs4277405 | ACE | 17 | 0.94 | RAS/vascular |
| rs199515 | WNT3/MAPT | 17 | 0.94 | Tau locus |
| rs616338 | ABI3 | 17 | 1.32 | Microglial actin regulation |
| rs12446759 / rs72824905 | PLCG2 | 16 | 0.95 / 0.74 | Microglial signaling; rs72824905 is protective |
| rs8025980 | SPPL2A | 15 | 0.96 | Intramembrane protease |
| rs602602 | MINDY2/ADAM10 | 15 | 0.94 | α-secretase |
| rs889555 | BCKDK/KAT8 | 16 | 0.95 | Histone acetyltransferase |
| rs4985556 | IL34 | 16 | 1.07 | Microglial survival cytokine |
| rs7401792 / rs12590654 | SLC24A4/RIN3 | 14 | 1.04 / 0.93 | Calcium transport / endosomal |
| rs2526377 | TSPOAP1 | 17 | 0.95 | Mitochondrial/microglia |
| rs2830489 | ADAMTS1 | 21 | 0.95 | Extracellular protease |
| rs5848 | GRN | 17 | 1.07 | Progranulin; lysosomal |
| rs7225151 | SCIMP | 17 | 1.08 | MHC signaling |
| rs6846529 | CLNK/HS3ST1 | 4 | 1.07 | Heparan sulfate |
Tier 3 - Novel Loci (from Bellenguez 2022 - first reported)
| SNP | Gene/Locus | Chr | Effect (OR) |
|---|---|---|---|
| rs141749679 | SORT1 | 1 | 1.38 |
| rs72777026 | ADAM17 | 2 | 1.06 |
| rs17020490 | PRKD3 | 2 | 1.06 |
| rs143080277 | NCK2 | 2 | 1.47 |
| rs139643391 | WDR12 | 2 | 0.94 |
| rs16824536 / rs61762319 | MME (neprilysin) | 3 | 0.92 / 1.16 |
| rs450674 | MAF | 16 | 0.96 |
| rs1140239 | DOC2A | 16 | 0.94 |
| rs56407236 | PRDM7 | 16 | 1.11 |
| rs16941239 | FOXF1 | 16 | 1.13 |
| rs35048651 | WDR81 | 17 | 1.06 |
| rs2242595 | MYO15A | 17 | 0.94 |
| rs10131280 | IGH gene cluster | 14 | 0.94 |
| rs12592898 | CTSH | 15 | 0.94 |
| rs3848143 | SNX1 | 15 | 1.05 |
Ancestry-Specific Notable SNPs
| SNP | Gene | Population | Notes |
|---|---|---|---|
| rs1815157 | EGFR | Chinese/East Asian | Novel; found in Ge et al. 2024 GWAS (PMID: 39023044) |
| Variants in KIAA2013, SLC52A3, TCN2 | Various | Chinese | Ancestry-specific loci |
| Variants in ABCA7, GPC6, AKAP9 | Various | African ancestry | Differ from European loci |
Key Points
- APOE ε4 (defined by rs429358 + rs7412) remains the single largest genetic risk factor by far, with OR ~3-12 depending on copy number.
- The 2026 consensus meta-analysis (PMID: 42237039, 128,681 cases, 849,833 controls) now identifies 91 confirmed loci, of which 16 are newly discovered.
- Many loci cluster around 4 biological pathways: amyloid/APP processing, tau, lipid metabolism, and microglial/immune function.
- TREM2 rs75932628 (R47H) is particularly important as a rare variant with a large effect size (OR ~2.4), driving intense therapeutic interest.
- Risk architecture differs by ancestry - many European GWAS hits do not replicate well in African or East Asian populations.
For a live, continuously updated catalog of all AD-associated variants, the NHGRI-EBI GWAS Catalog is the go-to resource.
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