Gene - Ensembl gene ID
GeneChr - Gene chromosome (GRCh38)
GenePos - Gene start position (GRCh38), may be the end of the gene relative to Gencode V32 annotation, depending on strand
GeneStrand - Gene strand
GeneSymbol - Gene HGNC symbol
SNP - Variant ID
SNPChr - Variant chromosome
SNPPos - Variant chromosome position (GRCh38)
SNPAlleles - Alleles for the variant. Format: allele1/allele2. Note that allele1 is not always the reference allele, and allele2 is not always the effect allele.
SNPEffectAllele - Effect allele that was used for calculating the QTL
SNPEffectAlleleFreq - Allele frequency of the effect allele
MetaP - Meta-analysis P-value (derived from sample size weighted Z-score meta-analysis)
MetaPN - Meta-analysis sample size
MetaPZ - Meta-analysis Z-score
MetaBeta - Meta-analysis beta; derived from meta-analysis Z-score and SNP effect allele frequency. See article methods/supplement for more details
MetaSE - Meta-analysis standard error, derived from meta-analysis Z-score and SNP effect allele frequency
NrDatasets - Number of datasets in which this QTL was tested, and over which meta-analysis was performed.
DatasetCorrelationCoefficients - Correlation coefficients for each dataset. Separated by semicolons. Order of datasets indicated within braces. 
DatasetZScores - Z-scores derived from dataset correlation coefficients, used in meta-analysis
DatasetSampleSizes - Sample sizes per dataset for this effect; used as weights for the meta-analysis
NrTestedSNPs - Number of SNPs tested for this gene - specific to TopEffects files
ProportionBetterPermPvals - Number of meta-analyzed p-values that are lower than MetaP in the permutation runs - specific for TopEffects files 
BetaDistAlpha - Beta distribution alpha parameter - specific for TopEffects files
BetaDistBeta - Beta distribution beta parameter - specific for TopEffects files
BetaAdjustedMetaP - Meta-analysis P-value adjusted using the beta-distribution that was fitted over the permuted p-value distribution; this was used to determine the significance using the q-values package - specific for TopEffects files
PvalueNominalThreshold - Nominal p-value threshold that can be used to determine which SNPs are significant for this gene: all SNPs tested for this gene that have a MetaP smaller than this threshold can be considered significant - specific for TopEffects files 
qval - Q-value estimate for this gene, determines significance of the top-effect; calculated using the BetaAdjustedMetaP values of all genes tested - specific for topEffects files