DOI: 10.5281/zenodo.4118403
title: Results for sQTL analysis for each brain region

description: This dataset is part of the manuscript: "<em>Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies</em>", by Lopes KP, Snijders GJL, Humphrey J, et al. Description of files: <em>MFG_eur_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - </em>Full <strong>nominal sQTL</strong> summary statistics from medial frontal gyrus (<strong>MFG</strong>)<em> </em>(gzip-compressed) <em>STG_eur_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz </em>- Full <strong>nominal sQTL</strong> summary statistics from superior temporal gyrus (<strong>STG</strong>) (gzip-compressed) <em>SVZ_eur_splicing_peer0_gene.cis_qtl_nominal_tabixed.tsv.gz -</em> Full <strong>nominal sQTL</strong> summary statistics from the subventricular zone (<strong>SVZ</strong>) (gzip-compressed) <em>THA_eur_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - </em>Full <strong>nominal sQTL</strong> summary statistics from the thalamus (<strong>THA</strong>) (gzip-compressed) <em>MFG_eur_splicing_peer5_cluster.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by intron cluster </strong>from medial frontal gyrus (<strong>MFG</strong>) (gzip-compressed) <em>STG_eur_splicing_peer5_cluster.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by intron cluster</strong> from superior temporal gyrus (<strong>STG</strong>)<em> </em>(gzip-compressed) <em>SVZ_eur_splicing_peer0_cluster.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by intron cluster</strong> from the subventricular zone (<strong>SVZ</strong>)<em> </em>(gzip-compressed) <em>THA_eur_splicing_peer5_cluster.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by intron cluster</strong> from the thalamus (<strong>THA</strong>)<em> </em>(gzip-compressed) <em>MFG_eur_splicing_peer5_gene.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by gene </strong>from medial frontal gyrus (<strong>MFG</strong>)<em> </em>(gzip-compressed) <em>STG_eur_splicing_peer5_gene.cis_qtl.txt.gz </em> - Full <strong>sQTL</strong> summary statistics <strong>permuted by gene</strong> from superior temporal gyrus (<strong>STG</strong>) (gzip-compressed) <em>SVZ_eur_splicing_peer0_gene.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by gene</strong> from the subventricular zone (<strong>SVZ</strong>)<em> </em>(gzip-compressed) <em>THA_eur_splicing_peer5_gene.cis_qtl.txt.gz - </em>Full <strong>sQTL</strong> summary statistics <strong>permuted by gene</strong> from the thalamus (<strong>THA</strong>) (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 <em>P</em>-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 <em>cis </em>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 <em>P</em>-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 &lt;= 0.5, -1 if not) pval_nominal - nominal <em>P</em>-value from linear regression slope - slope of the linear regression slope_se - standard error of the slope pval_perm - first permutation <em>P</em>-value directly obtained from the permutations with the direct method pval_beta - second permutation <em>P</em>-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 <em>P</em>-value threshold for calling a variant-gene pair significant for the group (cluster or gene, depending on the file) <strong>NOTE: </strong>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