These are the standard QTLtools (https://qtltools.github.io/qtltools/) output files with the following column names: The phenotype group ID (here a gene ID) The chromosome ID of the phenotype group The start position of the phenotype group The end position of the phenotype group The strand orientation of the phenotype group The top phenotype in the group (here an exon ID) The total number of phenotypes in the group (i.e. #exons) The total number of variants tested in cis The distance between the phenotype group and the tested variant (accounting for strand orientation) The ID of the top variant The chromosome ID of the top variant The start position of the top variant The end position of the top variant The number of degrees of freedom used to compute the P-values Dummy The first parameter value of the fitted beta distribution The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region) The nominal P-value of association between the top phenotype and the top variant in cis The corresponding regression slope The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the direct method (i.e. empirircal P-value) The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis I prefer to use the following short column names group_id pheno_chr pheno_start pheno_end strand phenotype_id group_size n_cis_snps distance snp_id snp_chr snp_start snp_end df dummy beta1 beta2 p_nominal slope p_perm p_beta