Can you give a list of SNPs that are associated with alzheimers?
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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