DOI: 10.5281/zenodo.5248757
title: Full expression and splicing QTL summary statistics for three human spinal cord segments

description: This dataset is part of the manuscript: <strong>"Integrative genetic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes</strong>" by Jack Humphrey, et al. The files below contain nominal and permuted quantitative trait loci (QTL) associations between common genetic variants derived from whole genome sequencing and either gene expression or splicing phenotypes generated from RNA-seq of post-mortem spinal cord sections. All QTLs were mapped with TensorQTL. Nominal association files are coordinate sorted, bgzip-compressed and tabix-indexed tab-separated variable files. Top association files are gzip-compressed tab-separated variable files. Sample sizes for each dataset are as follows: Cervical spinal cord n = 216. Lumbar spinal cord n = 197. Thoracic spinal cord n = 68. Description of files:<br> CervicalSpinalCord_expression_peer30_gene.cis_qtl.txt.gz - <strong>Top per-gene </strong>eQTL summary statistics from cervical spinal cord <br> CervicalSpinalCord_expression_peer30_gene.cis_qtl_nominal_tabixed.tsv.gz - <strong>Full nominal</strong> eQTL summary statistics from cervical spinal cord <br> CervicalSpinalCord_splicing_peer15_cluster.cis_qtl.txt.gz - <strong>Top per-cluster </strong>sQTL summary statistics from cervical spinal cord<br> CervicalSpinalCord_splicing_peer15_gene.cis_qtl_nominal_tabixed.tsv.gz - <strong>Full nominal</strong> sQTL summary statistics from cervical spinal cord<br> LumbarSpinalCord_expression_peer30_gene.cis_qtl.txt.gz - <strong>Top per-gene </strong>eQTL summary statistics from lumbar spinal cord<br> LumbarSpinalCord_expression_peer30_gene.cis_qtl_nominal_tabixed.tsv.gz -<strong> Full nominal</strong> eQTL summary statistics from lumbar spinal cord<br> LumbarSpinalCord_splicing_peer10_cluster.cis_qtl.txt.gz - <strong>Top per-cluster </strong>sQTL summary statistics from lumbar spinal cord<br> LumbarSpinalCord_splicing_peer10_gene.cis_qtl_nominal_tabixed.tsv.gz - <strong>Full nominal</strong> sQTL summary statistics from lumbar spinal cord<br> ThoracicSpinalCord_expression_peer10_gene.cis_qtl.txt.gz - <strong>Top per-gene </strong>eQTL summary statistics from thoracic spinal cord<br> ThoracicSpinalCord_expression_peer10_gene.cis_qtl_nominal_tabixed.tsv.gz - <strong>Full nominal</strong> eQTL summary statistics from thoracic spinal cord<br> ThoracicSpinalCord_splicing_peer5_cluster.cis_qtl.txt.gz - <strong>Top per-cluster </strong>sQTL summary statistics from thoracic spinal cord<br> ThoracicSpinalCord_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - <strong>Full nominal</strong> sQTL summary statistics from thoracic spinal cord als_snps_maf0.01_alleles.tsv.gz<strong> - Allele information</strong> for all SNPs tested in the eQTL and sQTL analysis Table columns are formatted as follows: Nominal QTL results include all SNP-gene pairs tested using either a 1Mb window from each side of the transcription start site (TSS) of the gene (eQTLs) or 100kb either side of the middle of the splicing cluster (sQTLs). Table columns are formatted as follows: phenotype_id - ensembl ID of the gene tested (GENCODE v30) for eQTL, or the ID of the splice junction for sQTLs, splicing junction position, splicing cluster id, and gene Ensembl id (GENCODE v30),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 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 Permuted QTL results include only the top SNP-gene association for each gene (eQTL) or cluster (sQTL). Table columns are formatted as follows: phenotype_id - ensembl ID of the gene tested (GENCODE v30), or the coordinates of the cluster, formatted as coordinate, splicing cluster id, and gene Ensembl id (GENCODE v30), separated by a colon num_var - total number of variants tested in <em>cis</em> 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 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 gene Allele Information for each variant: CHROM - chromosome position of the variant POS - position of the variant in the chromosome REF - reference allele (GRCh38) ALT - alternative allele (this is the <strong>effect</strong> allele in the eQTL and sQTL analysis) ID - variant id (rsid or chr:position:ref:alt)