Full expression and splicing QTL summary statistics for three human spinal cord segments

This dataset is part of the manuscript: "Integrative genetic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes" 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:
CervicalSpinalCord_expression_peer30_gene.cis_qtl.txt.gz - Top per-gene eQTL summary statistics from cervical spinal cord 
CervicalSpinalCord_expression_peer30_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal eQTL summary statistics from cervical spinal cord 
CervicalSpinalCord_splicing_peer15_cluster.cis_qtl.txt.gz - Top per-cluster sQTL summary statistics from cervical spinal cord
CervicalSpinalCord_splicing_peer15_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from cervical spinal cord
LumbarSpinalCord_expression_peer30_gene.cis_qtl.txt.gz - Top per-gene eQTL summary statistics from lumbar spinal cord
LumbarSpinalCord_expression_peer30_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal eQTL summary statistics from lumbar spinal cord
LumbarSpinalCord_splicing_peer10_cluster.cis_qtl.txt.gz - Top per-cluster sQTL summary statistics from lumbar spinal cord
LumbarSpinalCord_splicing_peer10_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from lumbar spinal cord
ThoracicSpinalCord_expression_peer10_gene.cis_qtl.txt.gz - Top per-gene eQTL summary statistics from thoracic spinal cord
ThoracicSpinalCord_expression_peer10_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal eQTL summary statistics from thoracic spinal cord
ThoracicSpinalCord_splicing_peer5_cluster.cis_qtl.txt.gz - Top per-cluster sQTL summary statistics from thoracic spinal cord
ThoracicSpinalCord_splicing_peer5_gene.cis_qtl_nominal_tabixed.tsv.gz - Full nominal sQTL summary statistics from thoracic spinal cord

als_snps_maf0.01_alleles.tsv.gz - Allele information 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 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 (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 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

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 effect allele in the eQTL and sQTL analysis)
• ID - variant id (rsid or chr:position:ref:alt)