Supplementary Data for Sinnott-Armstrong and Naqvi, eLife 2020

This folder contains supplementary tables and GWAS summary statistics described in: Updated 1/12/21 Nasa Sinnott-Armstrong, Sahin Naqvi, Manuel Rivas, and Jonathan K Pritchard. GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background. bioRxiv 2020. Supplementary Files 1-4 contain lead SNPs from loci with genome-wide signficiant associations for each of the four primary phenotypes considered (Urate, IGF-1, Male testosterone, Female testosterone for Files 1-4, respectively) See paper for details on how lead SNPs were identified. Supplementary Files 8-10 contain designated "core" genes and their corresponding subpathways for each of the three traits (Urate, IGF-1, Testosterone) See paper for details on how core genes and pathways were designated. summary_enrich_pathways.orig.hess.tsv contains estimates of heritability (from HESS) for the core pathways in Supplementary Files 8-10 all_hits_msiggenes.bed contains gene coordinates for all genes used in the analysis (i.e. background set for enrichment analyses) ORIG_RAW_{trait}_{all|male|female}.sumstats.tsv.gz are summary statistics for the primary GWAS performed and used to create Manhattan plots and lead SNPs in Supplemental Tables 1-4 for downstream analyses free_androgen_phenotypes.{male|female}.{trait}.glm.linear.gz and lh1_all.log.glm.filtered.maf01.info07.tsv.gz are summary statistics for secondary analyses of testosterone-related phenotypes (i.e. Figure 7B,C, Figures S9,10) Note that the free_androgen_phenotypes sumstats are derived using a minimal set of covariates relative to the ORIG_RAW sumstats due to the derivation from albumin, SHBG, and testosterone, and the difference in batch between these