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.