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. Author manuscript; available in PMC: 2015 Jul 2.
Published in final edited form as: Neuron. 2014 Jul 2;83(1):11–26. doi: 10.1016/j.neuron.2014.05.041

Table 1.

SNP Gene MAF Odds Ratio Known function Related AD Risk Genes Potential Effects on APP and Tau Pathways Gene Expression
APP Neurite outgrowth, adhesion and axonogenesis Cleavage yields Aβ APP processing
PSEN1 Component of catalytic subunit of gamma-secretase complex. Proteolytic cleavage of integral membrane proteins Cleaves APP APP processing
PSEN2 Component of catalytic subunit of gamma-secretase complex. Proteolytic cleavage of integral membrane proteins Cleaves APP APP processing
APOE Mediates binding, internalization and catabolism of lipoproteins SORL1 Aβ clearance Lipid Metabolism
ADAM10 Proteolytic cleavage of integral membrane proteins Cleaves APP APP processing
rs6656401 CR1a 0.197 1.18 Mediates cellular binding of immune complexes that activate complement Aβ clearance Immune Response Increased
rs6733839 BIN1b 0.409 1.22 Regulation of endocytosis of synaptic vesicles SLC24A4 & RIN3 Mediates tau toxicity Synapse function Increased
rs10948363 CD2AP 0.266 1.1 Scaffold molecule regulating actin cytoskeleton INPP5D & CASS4 Mediates tau toxicity Synapse function & Endocytosis No change
rs11771145 EPHA1c 0.338 0.9 Brain and neural development. Angiogenesis, cell proliferation, and apoptosis N/A Immune Response & Neural Development No change
rs9331896 CLU 0.379 0.86 Chaperone. Regulation of cell proliferation. PTK2B Aβ clearance Immune Response & Lipid Metabolism Increased
rs983392 MS4A6Ad 0.403 0.9 Signal transduction N/A Immune Response No change
rs10792832 PICALMe 0.358 0.87 AP2-dependent clathrin mediated endocytosis APP trafficking & Aβ clearance Synapse function & Endocytosis No change
rs4147929 ABCA7f 0.19 1.15 Lipid homeostasis. Phagocytosis of apoptotic cells by macrophages Aβ clearance Immune Response & Lipid Metabolism Increased
rs3865444 CD33 0.307 0.94 Mediates sialic acid-dependent binding to cells Aβ clearance Immune Response Increased
rs9271192 HLA-DRB5 HLA- DRB1g 0.276 1.11 Immunocompetence and histocompatibility N/A Immune Response N/A
rs28834970 PTK2B 0.366 1.1 Induction of long term potentiation in hippocampus CLU N/A Synapse function & Neural Development N/A
rs11218343 SORL1 0.039 0.77 APOE receptor. Binds LDL and RAP and mediates endocytosis of the lipids to which it binds APOE APP trafficking Lipid Metabolism, Synapse Function & Endocytosis Decreased
rs10498633 SLC24A4 & RIN3 0.217 0.91 Brain and neural development (SLC24A4); Stimulates & stabilizes GTP-Rab5 in protein transport from plasma membrane to early endosome (RIN3) BIN1 N/A Neural Development, Synapse Function & Endocytosis N/A
rs8093731 DSG2h 0.017 0.73 Mediates cell-cell junctions between epithelial and other cell type. N/A N/A N/A
rs35349669 INPP5D 0.488 1.08 Negative regulator of myeloid cell proliferation and survival CD2AP N/A Immune Response N/A
rs190982 MEF2C 0.408 0.93 Controls synapse formation during activity-dependent refinement of synaptic connectivity and facilitates hippocampal-dependent learning and memory N/A Neural Development, Synapse Function & Immune Response N/A
rs2718058 NME8i 0.373 0.93 Ciliary functions N/A N/A N/A
rs1476679 ZCWPW1 & NYAP1j 0.287 0.91 Epigenetic regulation (ZCWPW1); Brain and neural development (NYAP1) N/A Neural Development N/A
rs10838725 CELF1 & MADDk 0.316 1.08 Regulates pre-mRNA splicing (CELF1); Long-term neuronal viability (MADD) Mediates tau toxicity Neural Development N/A
rs17125944 FERMT2 0.092 1.14 Actin assembly and cell shape and mediator of angiogenesis Mediates tau toxicity Cytoskeleton & Axonal transport N/A
rs7274581 CASS4l 0.083 0.88 Docking protein in tyrosine-kinase signaling involved in cell adhesion and spreading CD2AP N/A Cytoskeleton & Axonal transport N/A
rs75932628 TREM2 0.049 2.55 Immune response, triggers production of inflammatory cytokines Aβ clearance Immune Response N/A
rs145999145 PLD3 0.06 2.75 Unknown APP trafficking and cleavage Unknown Increased

Additional genes located within GWAS loci:

A, CR2, CR1L

B, CYP27C1

C, LOC285965, TAS2R60

D, MS4A3, MS4A2, MS4A6A, MS4A4A, MS4A6E

E, EED

F, CNN2, POLR3E, GPX4

G, HLA-DRB6, HLA-DQA1, HLA-DQB1

H, GSG2

I, GPR141

J, PMS2P1, PILRB, PILRA, C7ORF61, C7ORF47, MEPCE

K, SLC39A13, PSMC3, NDUFS3, KBTBD4, PTPMT1, MTCH2, AGBL2, FNBP4, NUP160

L, C20ORF43, CSTF1