The summary statistic files contains the following columns: phenotype_id chr pos snp_id distance p_nominal beta The *.permuteted.txt.gz files are from the permutation pass of FastQTL and contains the following columns: phneotype_id - ID of the tested molecular phenotype (in this particular case, the gene ID) n_snps - Number of variants tested in cis for this phenotype beta1 - MLE of the shape1 parameter of the Beta distribution beta2 - MLE of the shape2 parameter of the Beta distribution dummy - Dummy [To be described later] snp_id - ID of the best variant found for this molecular phenotypes (i.e. with the smallest p-value) distance - Distance between the molecular phenotype - variant pair p_nominal - The nominal p-value of association that quantifies how significant from 0, the regression coefficient is beta - The slope associated with the nominal p-value of association [only in version > v2-184] p_perm - A first permutation p-value directly obtained from the permutations with the direct method. This is basically a corrected version of the nominal p-value that accounts for the fact that multiple variants are tested per molecular phenotype. p_beta - A second permutation p-value obtained via beta approximation. We advice to use this one in any downstream analysis.