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Table 3 Functional description and expression of genes associated with the top 30 dataset SNPs in the TGen dataset

From: Identifying genetic interactions associated with late-onset Alzheimer’s disease

Gene symbol (SNP) Name Description Differential expression in AD 1-SNP model rank p value of pair from PLINK
APOE2 (rs7412) Apolipoprotein E APOE is essential for the normal catabolism of triglyceride-rich lipoprotein constituents. Known risk factor for LOAD. Overexpressed [38] 1 0.05993
APOC1 (rs4420638) Apolipoprotein C-1 Appears to modulate the interaction of APOE with beta-migrating VLDL. Binds free fatty acids. Overexpressed [38] 3 0.705
C10orf11 (rs7079348) Chromosome 10 open reading frame 11 A brain-expressed gene. Haploinsufficiency of C10orf11 contributes to the cognitive defects in 10q22 syndrome [47]. - 4 0.009623
VWC2 (rs10499687) von Willebrand factor C domain-containing protein 2 (Brorin, Brain-specific chordin-like protein) Encodes a secreted bone morphogenic protein (BMP) antagonist. The encoded protein is possibly involved in neural function and development and may have a role in cell adhesion. BMP-6 is increased in AD brains and leads to impaired neurogenesis [39]. Underexpressed [48] 12 0.7698
PSD3 (rs17126808) Pleckstrin and Sec7 domain containing 3 Guanine nucleotide exchange factor for ARF6 that contributes to the regulation of dendritic branching [49]. Overexpressed [38] 34 0.001623
GXYLT2 (rs3732443) Glucoside xylosyltransferase 2 Elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins [49], which are substrates of γ-secretase, the enzyme involved in amyloid beta production [50]. Underexpressed in a murine AD model [51] 6 0.211
GABBR2 (rs2779550) Gamma-aminobutyric acid (GABA) B receptor, 2 Target for autophagy regulation in neurodegenerative diseases [52]. Overexpressed [38] 391 0.0002945
ENPP2 (rs16892852) Ectonucleotide pyrophosphatase/phosphodiesterase 2 Hydrolyzes lysophospholipids to produce lysophosphatidic acid (LPA) in extracellular fluids. Predominantly expressed in brain, placenta, ovary, and small intestine. Secreted by most body fluids including serum and cerebrospinal fluid [49]. Overexpressed [38] 92 0.04851
GLP1R (rs910171) Glucagon-like peptide 1 receptor Member of the glucagon receptor family (also includes glucagon, GLP-2, secretin, GHRH and GIP receptors).In the brain located in hypothalamus and brainstem. Protective against amyloid beta accumulation in rats [53]. Overexpressed [38] 193 0.01462
MOSC1 (rs746767) MOCO sulphurase C-terminal domain containing 1 A mitochondrial oxidoreductase, cofactor: molybdenum, is expressed in the brain. MOSC1 is a target for miR-129-5p, like GABBR2, and miR-155, like PICALM. - 66 0.04507
TM4SF20 (rs4408717) Transmembrane 4 L six family member 20 Tetraspannin superfamily member. Tetraspanins are often thought to act as scaffolding proteins, anchoring multiple proteins to one area of the cell membrane. Other tetraspanin superfamily members have been implicated in Notch signaling and g-secretase activity modulation [54]. - 95 0.004495
  1. 1-SNP model rank: rank of the corresponding SNP in terms of univariate 1-SNP model score.