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    Additional file 1: Table S1. of Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer’s disease

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    Sample characteristics. Table S2. Association P values of Alzheimer disease loci previously established by GWAS in univariate and pleiotropy association tests of neuropathological features. Table S3. Association of cis-eQTL for HDAC9 in the Mayo Clinic brain expression genome-wide association study (eGWAS). rs79524815 was not available in the Mayo Clinic brain eGWAS, so proxy SNPs that are in LD (D′ > 0.90) with rs79524815 were used for the eQTL test with HDAC9 expression. Table S4. Association of expression of SNPs for TRAPPC12-AS1 and ADI1 with neuropathological traits and gene expression in the GTEx portal database. Table S5. Association results from the trivariate pleiotropy model of neuritic plaque (NP), neurofibrillary tangles (NFT), and cerebral amyloid angiopathy (CAA) for study-wide significant SNPs in the bivariate pleiotropy model. Table S6. Results of differential gene expression analysis by brain region among AD cases and controls for AD loci previously established by GWAS in RNA-Seq and microarray analysis. Figure S1. Quantile-quantile plots of observed (y-axis) vs. expected (x-axis) P values of all SNPs (black dots) and after excluding SNPs in APOE region (blue dots) for the pleiotropy analysis of (a) NP and NFT, (b) NP and CAA, and (c) NFT and CAA using the O’Brien method [10]. Figure S2. Manhattan plots showing genome-wide pleiotropy analyses of (a) NP and NFT, (b) NP and CAA, and (c) NFT and CAA using the O’Brien method [10]. Red dashed line represents the genome-wide significance threshold of P < 5.0 × 10−−8. Loci achieving genome-wide significance are highlighted in red, and known AD genes that attained at least a moderate significance level (P < 10−−4) are highlighted in gold. Figure S3. Regional association plots of genes, including TRAPPC12, TRAPPC12-AS1, and ADI1, on chromosome 2 from the joint model of NFT and CAA. Figure S4. Genome-wide trivariate pleiotropy analysis of NP, NFT, and CAA. (a) Quantile-quantile plot. (b) Manhattan plot. (DOCX 1028 kb
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