Results for sQTL 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_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from medial frontal gyrus (MFG) (gzip-compressed)

STG_eur_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from superior temporal gyrus (STG) (gzip-compressed)

SVZ_eur_splicing_peer0_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from the subventricular zone (SVZ) (gzip-compressed)

THA_eur_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from the thalamus (THA) (gzip-compressed)

MFG_eur_splicing_peer5_cluster.cis_qtl.txt.gz - Full sQTL summary statistics permuted by intron cluster from medial frontal gyrus (MFG) (gzip-compressed)

STG_eur_splicing_peer5_cluster.cis_qtl.txt.gz - Full sQTL summary statistics permuted by intron cluster from superior temporal gyrus (STG) (gzip-compressed)

SVZ_eur_splicing_peer0_cluster.cis_qtl.txt.gz - Full sQTL summary statistics permuted by intron cluster from the subventricular zone (SVZ) (gzip-compressed)

THA_eur_splicing_peer5_cluster.cis_qtl.txt.gz - Full sQTL summary statistics permuted by intron cluster from the thalamus (THA) (gzip-compressed)

MFG_eur_splicing_peer5_gene.cis_qtl.txt.gz - Full sQTL summary statistics permuted by gene from medial frontal gyrus (MFG) (gzip-compressed)

STG_eur_splicing_peer5_gene.cis_qtl.txt.gz  - Full sQTL summary statistics permuted by gene from superior temporal gyrus (STG) (gzip-compressed)

SVZ_eur_splicing_peer0_gene.cis_qtl.txt.gz - Full sQTL summary statistics permuted by gene from the subventricular zone (SVZ) (gzip-compressed)

THA_eur_splicing_peer5_gene.cis_qtl.txt.gz - Full sQTL summary statistics permuted by gene from the thalamus (THA) (gzip-compressed)

Nominal QTL results include all SNP-junction pairs tested (using a 100kb window from the center of each intron cluster). Table columns are formatted as follows:

phenotype_id - id composed by splicing junction position, splicing cluster id, and gene Ensembl id (GENCODE v30) each separated by a colon

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

chr - chromosome of the SNP (hg38)

pos - position for the SNP in the chromosome (hg38)

Permuted QTL results include only the top SNP-junction association (by cluster or gene level). Table columns are formatted as follows:

phenotype_id - id composed by splicing junction position, splicing cluster id, and gene Ensembl id (GENCODE v30), each separated by a colon

num_var - total number of variants tested in cis per group (cluster or gene, depending on the file)

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 top 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 group (cluster or gene, depending on the file)

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