Results for eQTL analysis for each brain region

This dataset is part of the manuscript: "Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies", by Lopes KP, Snijders GJL, Humphrey J, et al.

Description of files:

MFG_eur_expression_peer10.cis_qtl_nominal.txt.gz - Full nominal eQTL summary statistics from medial frontal gyrus (MFG) (gzip-compressed)

STG_eur_expression_peer10.cis_qtl_nominal.txt.gz - Full nominal eQTL summary statistics from superior temporal gyrus (STG) (gzip-compressed)

SVZ_eur_expression_peer5.cis_qtl_nominal.txt.gz - Full nominal eQTL summary statistics from subventricular zone (SVZ) (gzip-compressed)

THA_eur_expression_peer10.cis_qtl_nominal.txt.gz - Full nominal eQTL summary statistics from thalamus (THA) (gzip-compressed)

MFG_eur_expression_peer10.cis_qtl.txt.gz - Full permuted eQTL summary statistics from medial frontal gyrus (MFG) (gzip-compressed)

STG_eur_expression_peer10.cis_qtl.txt.gz - Full permuted eQTL summary statistics from superior temporal gyrus (STG) (gzip-compressed)

SVZ_eur_expression_peer5.cis_qtl.txt.gz - Full permuted eQTL summary statistics from subventricular zone (SVZ) (gzip-compressed)

THA_eur_expression_peer10.cis_qtl.txt.gz - Full permuted eQTL summary statistics from thalamus (THA) (gzip-compressed)

Nominal QTL results include all SNP-gene pairs tested (using a 1Mb window from each side of the transcription start site (TSS) of a gene). Table columns are formatted as follows:

phenotype_id - ensembl ID of the gene tested (GENCODE v30)

variant_id - SNP tested for association (rsid or chr:position:ref:alt)

tss_distance - distance of the SNP to the gene transcription start site (TSS)

maf - minor allele frequency in MiGA cohort

ma_samples - number of samples carrying the minor allele

ma_count - total number of minor alleles across individuals

pval_nominal - nominal P-value from linear regression

slope - slope of the linear regression

slope_se - standard error of the slope

Permuted QTL results include only the top SNP-gene association for each gene. Table columns are formatted as follows:

phenotype_id - ensembl ID of the gene tested (GENCODE v30)

num_var - total number of variants tested in cis

beta_shape1 - first parameter value of the fitted beta distribution

beta_shape2 - second parameter value of the fitted beta distribution

true_df - effective degrees of freedom the beta distribution approximation

pval_true_df - empirical P-value for the beta distribution approximation

variant_id - ID of the top variant (rsid or chr:position:ref:alt)

tss_distance - distance of the SNP to the gene transcription start site (TSS)

ma_samples - number of samples carrying the minor allele

ma_count - total number of minor alleles across individuals

maf -minor allele frequency in MiGA cohort

ref_factor - flag indicating if the alternative allele is the minor allele in the cohort (1 if AF <= 0.5, -1 if not)

pval_nominal - nominal P-value from linear regression

slope - slope of the linear regression

slope_se - standard error of the slope

pval_perm - first permutation P-value directly obtained from the permutations with the direct method

pval_beta - second permutation P-value obtained via beta approximation. This is the one to use for downstream analysis

qval - Storey q-value derived from pval_beta (FDR adjusted)

pval_nominal_threshold - nominal P-value threshold for calling a variant-gene pair significant for the gene

NOTE: The effect sizes of eQTLs and sQTL are defined as the effect of the alternative allele (ALT) relative to the reference (REF) allele in the human genome reference (GRCh38). A file containing that information for all alleles tested is available at 10.5281/zenodo.4301005