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Table 2 Functional description and expression of genes associated with the top 30 dataset SNPs in the ADRC dataset

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

Gene symbol(SNP) Name Description Expression in AD 1-SNP model rank p value of pair from PLINK
APOC1 (rs4420638) Apolipoprotein C-I Appears to modulate the interaction of APOE with beta-migrating VLDL. Binds free fatty acids. Overexpressed [38] 2 0.3326
TOMM40 (rs157582) Translocase of outer mitochondrial membrane 40 homolog Channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex, essential for protein import into mitochondria. Underexpressed [38] 3 0.4139
APOE (rs7412) Apolipoprotein E APOE is essential for the normal catabolism of triglyceride-rich lipoprotein constituents. Known risk factor for LOAD. Overexpressed [38] 5 0.8172
SNTG1 (rs16914489) Gamma-1-syntrophin Specifically expressed in the brain, highly expressed in the cortex. Organizes the subcellular localization of a variety of proteins. Overexpressed [38] 24906 0.004546
TMEM217 (rs9470543) Transmembrane protein 217 Expressed in the brain - 4584 0.004643
SMAD6 (rs3934907) Mothers against DPP homolog 6 Negative regulation of BMP and TGF-beta/activin-signaling. BMP-6 is increased in AD brains and leads to impaired neurogenesis [39]. Reduced TGF-beta signaling is involved in neurodegeneration and promotes AD like changes in mice [40]. Underexpressed [38] 41282 0.0000998
NPAS3 (rs4981180) Neuronal PAS domain protein 3. Transcription factor. May regulate genes involved in neurogenesis. Associated with schizophrenia and mental retardation Overexpressed [38] 1086 0.1225
NTM (rs11222692) Neurotrimin May promote neurite outgrowth and adhesion. NTM lies at locus 11q25, which has been associated with AD [41],[42]. Overexpressed [38] 12209 0.1422
PPAPDC1A (rs4752432) Phosphatidic acid phosphatase type 2 domain containing 1A - - 6852 0.3963
NPFF (rs8192593) Neuropeptide FF-amide peptide precursor Modulation of morphine-induced antinociception. - 3981 0.1251
SLC25A21 (rs7140725) Solute carrier family 25 Known also as ornithine decarboxylase (ODC). Mitochondrial oxoadipate carrier, part of polyamine synthesis pathway. Overexpressed [43],[44] 444 0.06767
RAB23 (rs182662) Member RAS oncogene family Intracellular protein transportation. Regulated by miRNA155, which also regulates PICALM (a known AD association). Underexpressed [38] 96 0.08251
UNC5D (rs4577954) unc-5 homolog D (C. elegans) Netrin receptor: netrins are secreted proteins that direct axon extension and cell migration during neural development. APP also binds Netrin-1 and in transgenic mice this suppresses amyloid beta peptide production [45]. - 63972 0.6731
CHD9 (rs3852742) Chromodomain helicase DNA binding protein 9, PPARA -interacting complex 320 kDa protein Transcriptional co-activator for PPARA. The APOE gene promoter has a binding site for PPAR alpha. Low CHD9 activity could reduce APOE levels. Increase in APOE transcription has been shown to clear amyloid beta in AD mouse models [46]. Overexpressed [38] 1061 0.04696
CNTN4 (rs9819935) Contactin 4, Brain-derived immunoglobulin superfamily protein 2 Mainly expressed in brain. Neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Associated with Spinocerebellar Ataxia, Amyotrophic Lateral Sclerosis, 3p deletion syndrome. - 2149 0.002386
  1. 1-SNP model rank: rank of the corresponding SNP in terms of univariate 1-SNP model score.