Background This data set provides genomic reference information extracted from the 1000 Genomes Project for calculating conditional and conjunctional false discovery rates for genetic variants that are pleiotropic for pairs of phenotypes. genref.zip is preprocessed information that can be directly used with the R package cfdr.pleio, available from github genref_rawdata.zip contains raw data downloaded from the 1000 Genome projects. You only need to download this if you want to re-create or modify the preprocessed reference data from above. The original code for creating the preprocessed data is available from github. Usage See the instructions at the two named github repositories for details. Credit The code for generating the preprocessed reference data as well as some auxiliary information were forked from the MATLAB package pleiofdr The original concept of the conditional and conjunctional FDR were described in Andreassen et al. (2013). For a recent overview of methods and applications, see Smeland et al. (2019).