Additional file 1 of Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer’s disease related proteins

Additional file 1: Table S1. Description of Dataset. Table S2. Description of Biochemical Measures. Table S3. Summary Statistics for SNPs with a p-value < 1x10E-5 in all biochemical measures. Table S4. Estimated proportion of biochemical variance explained by GWS index SNPs. Table S5. Additional association model results for the GWS loci. Table S6. GWAS Summary statistics for all APOE index variants across phenotypes. Table S7. Description of Independent AMP-AD and Mayo Expansion Datasets. Table S8. Concordance between Imputed GWAS genotypes and Taqman/Sequencing genotypes. Table S9. Additional Annotations of GWS loci. Table S10. Analysis of GWS variants in the ADNI cohort. Table S11. Differentially expressed genes in two or more brain regions proximal to GWS variants in the AMP-AD RNAseq datasets. Table S12. Cell type specific differential expression of genes proximal to GWS variants. Table S13. Analysis of Significant AD GWAS SNPs from Kunkel et al 2019. Table S14. TaqMan Assays used for genotyping key variants. Figure S1. Histograms of biochemical measures. Figure S2. Circular Manhattan Plots with no GWS SNPs. Figure S3. Forest Plots. Figure S4. Summary of gene regulatory annotations for each GWS locus. Figure S5. Population Substructure via Eigenstrat Analysis. Figure S6. Quantile-Quantile (QQ) Plots of biochemical measure GWAS. Figure S7. Datasets used for manuscript analytics.

补充文件1：表S1 数据集说明；表S2 生化指标说明；表S3 所有生化指标中p值<1×10^-5的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）汇总统计量；表S4 全基因组显著（Genome-Wide Significant, GWS）索引单核苷酸多态性对生化变异的解释比例估计；表S5 全基因组显著位点的附加关联模型结果；表S6 各表型下载脂蛋白E（Apolipoprotein E, APOE）索引变异的全基因组关联研究（Genome-Wide Association Study, GWAS）汇总统计量；表S7 独立AMP-AD与Mayo扩展数据集说明；表S8 基因型填充的全基因组关联研究基因型与Taqman/测序基因型的一致性分析；表S9 全基因组显著位点的附加注释；表S10 阿尔茨海默病神经影像倡议（Alzheimer's Disease Neuroimaging Initiative, ADNI）队列中全基因组显著变异的分析；表S11 AMP-AD RNA测序（RNA Sequencing, RNA-seq）数据集中共2个及以上脑区域内靠近全基因组显著变异的差异表达基因；表S12 靠近全基因组显著变异的基因的细胞类型特异性差异表达分析；表S13 Kunkel等人2019年研究中的显著阿尔茨海默病（Alzheimer's Disease, AD）全基因组关联研究单核苷酸多态性分析；表S14 用于关键变异基因分型的TaqMan检测试剂盒；图S1 生化指标的直方图；图S2 无全基因组显著单核苷酸多态性的环形曼哈顿图；图S3 森林图；图S4 各全基因组显著位点的基因调控注释汇总；图S5 基于Eigenstrat分析的群体分层；图S6 生化指标全基因组关联研究的分位数-分位数（Quantile-Quantile, QQ）图；图S7 本研究手稿分析所用数据集汇总