PRISM full results: Predicted and labeled variant-trait effects

PRISM predicted significant genetic variant effects in a framework of 70 heritable traits from UK Biobank. Significant variant-trait effects are labeled with confounder pleiotropy, vertical pleiotropy, or direct effect. Each line of the file represents a variant-trait effect, so a genetic variant may appear on multiple lines.

Columns description:variant_hg19: Genomic variant coordinates (CHR:POS:REF:ALT) in the hg19/GRCh37 genome reference build.rsid: rsID number of the genetic variant.Pval_PRISM: P-value of the variant-trait effect computed by PRISM.FullPleio: Pleiotropy of the variant predicted by PRISM, indicating "Direct Effect" for direct effects; For vertical effects, indicates V:Trait1:Trait2:etc, with Trait1/Trait2/etc traits with vertical effect on the main trait through this variant;  For confounder effects, indicates U:Trait1:Trait2:etc, with Trait1/Trait2/etc traits sharing a confounder with the main trait through this variant. SynthPleio: Summary of the pleiotropy of the variant, simply describing the type of pleiotropy.Pval_GWASUKBB: Original p-value of the variant-trait association from UKBB GWAS summary statistics of the main trait.Trait_UKBB: Main trait affected by the variant effect, represented by the UKBB trait code.TraitName_UKBB: Main trait affected by the variant effect, represented by the UKBB trait name.

Please refer to the manuscript and github for further information:https://www.medrxiv.org/content/10.1101/2024.06.01.24308193https://github.com/martintnr/PRISM

v2: updated nomenclature.v3: added LHC-MR results.v4: revised results after review