https://github.com/RajLabMSSM/SingleBrain Full associations and top association summary statistics for cis-eQTLs mapped in the human brain single-nucleus RNA seq cohort(Fujita et al.[PMID: 38514782]) using SAIGE-QTL[PMID: 38798318], as part of the "SingleBrain" project. Sample size = 402 European ancestry donors. Each file has the following naming convention: {Cell type}_eqtl_{ASSOC}.tsv.gz References The following reference was used for mapping phenotypes: 1. GENCODE - GENCODE v38 comprehensive transcripts (https://www.gencodegenes.org/human/release_38.html) Cell type The following brain 7 major cell types were tested for genetic association: Ast: astrocytes End: endothelial cells Ext: excitatory neurons IN: inhibitory neurons MG: microglia OD: oligodendrocytes OPC: oligodendrocyte progenitor cell All phenotype matrices were scaled and centered and then quantile normalized. Associations Top associations (top_assoc.tsv.gz) list the SNP-feature pair with the lowest adjusted P-value (ACAT_P) for that feature. Full associations (full_assoc.tsv.gz) list all tested SNP-feature pairs. Data dictionary The columns of the two association files only differ by the presence of the ACAT_P column in the top associations. feature: the phenotype being tested CHR: chromosome POS: position (hg38) MarkerID: the genetic variant being tested Allele1: reference allele Allele2: alternate allele AC_Allele2: Alternate allele count AF_Allele2: Alternate allele frequency in the sample MissingRate: genotype missing rate BETA: Effect size estimate (per allele effect) SE: Standard error of beta Tstat: T-statistic for the effect size var: Variance of the score test statistic p.value: P-value p.value.NA: P-value computed using a normal approximation (Wald or score test), not SPA. Is.SPA: Whether the Saddlepoint Approximation (SPA) converged (TRUE/FALSE) N: Sample size used in the test p_bonf: P-value adjusted for the number of variants tested in that feature (Bonferroni) p_FDR: P-value adjusted for the number of variants tested in that feature (FDR) ACAT_P: Aggregated Cauchy Association Test (ACAT) p-value, which is a gene-level p-value combining multiple single-variant p-values for a given gene or region.