Results for eQTL and sQTL meta-analysis and colocalization

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:

COLOC_supp_table_all_results.tsv.gz - Table with results from COLOC (gzip-compressed). Table columns are formatted as follows:

disease - disease name (Alzheimer’s disease - AD, Bipolar Disorder - BPD, Multiple sclerosis - MS, Parkinson’s disease - PD, Schizohphrenia - SCZ)

GWAS - GWAS study (IMSGC_2019, Jansen_2018, Kunkle_2019, Lambert_2013, Marioni_2018, Nalls23andMe_2019, Ripke_2014, Stahl_2019)

locus - locus id according to each GWAS study

GWAS_SNP - SNP reported in the GWAS study

GWAS_P - P-value of the GWAS_SNP reported in the GWAS study

GWAS_chr - chromosome of the GWAS_SNP (hg38)

GWAS_pos - genomic position in the chromosome of the GWAS_SNP (hg38)

QTL - id for the QTL study

type - the type of QTL (eQTL or sQTL)

QTL_SNP - SNP id from the QTL association

QTL_P - P-value for the QTL association 

QTL_Beta - Slope (beta) for the QTL association

QTL_MAF - minor allele frequency for the QTL_SNP in each QTL study. If not available, values were obtained from the European superpopulation of 1000 Genomes phase 3

QTL_chr - chromosome for the QTL_SNP (hg38)

QTL_pos - genomic position in the chromosome of the QTL_SNP (hg38)

QTL_junction - splicing junction tested in the association (for sQTLs only)

QTL_Gene - gene name for the QTL association

QTL_Ensembl - Ensembl gene id for the QTL_gene (GENCODE v30)

nsnps - number of SNPs tested 

PP.H0.abf - posterior probability for H0 (no causal variant)

PP.H1.abf - posterior probability for H1 (causal variant for trait 1 only)

PP.H2.abf - posterior probability for H2 (causal variant for trait 2 only)

PP.H3.abf - posterior probability for H3 (two distinct causal variants)

PP.H4.abf - posterior probability for H4 (one common causal variant)

cell_type - cell type of the QTL study

SNP_distance - the absolute distance between GWAS_SNP and QTL_SNP

LD - linkage disequilibrium between the GWAS_SNP and the QTL_SNP according to 1000 genomes phase 3 European reference panel 3 (only for PP4>0.5, -Inf otherwise)

mashR_lfsr_eQTL.txt.gz - mashR results for eQTL (gzip-compressed). Table columns are formatted as follows:

ensembl_snp - Ensembl ID and the SNP prioritized by mashR (best SNP per gene)

MFG_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the MFG region

STG_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the STG region

SVZ_eur_expression_peer5.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the SVZ region

THA_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the THA region

mashR_lfsr_eQTL.txt.gz - mashR results for sQTL (gzip-compressed). Table columns are formatted as follows:

pos_ensembl_rsnp - splicing junction coordinates, Ensembl ID, and SNP ID prioritized by mashR (best SNP per junction)

MFG_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the MFG region

STG_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the STG region

SVZ_eur_rsplicing_peer0_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the SVZ region

THA_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the THA region

out_mfg_stg_svz_tha.metasoft.gz - METASOFT results for eQTLs meta-analysis from MiGA four brain regions (gzip-compressed). Table columns are formatted as follows:

RSID - Id composed by gene Ensembl and SNP ID separated by an underscore for each gene-SNP pair tested in the eQTL study

#STUDY - number of studies included in the meta-analysis

PVALUE_FE - P-value of the fixed-effects model (FE) according to METASOFT

BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT

STD_FE - Standard error of BETA_FE

PVALUE_RE - P-value of the random effects model (RE) according to METASOFT

BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT

STD_RE - Standard error of BETA_RE

PVALUE_RE2 - P-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT

STAT1_RE2 - RE2 statistic mean effect part

STAT2_RE2 - RE2 statistic heterogeneity part

PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)

I_SQUARE - I-square heterogeneity statistic

Q - Cochran's Q statistic

PVALUE_Q - Cochran's Q statistic's P-value

TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird

PVALUES_OF_STUDIES(Tab_delimitered) - P-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA

MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA

out_miga_young_mynd_fairfax.metasoft.gz - METASOFT results for eQTL meta-analysis from MiGA four brain regions plus microglia eQTL from Young et al. (2019), and monocytes eQTL from Navarro et al. (2020) and Fairfax et al. (2014) (gzip-compressed). Table columns are formatted as follows:

RSID - Id composed by gene Ensembl and SNP ID separated by an underscore for each gene-SNP pair tested in the eQTL study

#STUDY - number of studies included in the meta-analysis

PVALUE_FE - P-value of the fixed-effects model (FE) according to METASOFT

BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT

STD_FE - Standard error of BETA_FE

PVALUE_RE - P-value of the random effects model (RE) according to METASOFT

BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT

STD_RE - Standard error of BETA_RE

PVALUE_RE2 - P-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT

STAT1_RE2 - RE2 statistic mean effect part

STAT2_RE2 - RE2 statistic heterogeneity part

PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)

I_SQUARE - I-square heterogeneity statistic

Q - Cochran's Q statistic

PVALUE_Q - Cochran's Q statistic's P-value

TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird

PVALUES_OF_STUDIES(Tab_delimitered) - P-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA, 5-Young et al., 6-Navarro et al., 7-Fairfax et al.

MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA, 5-Young et al., 6-Navarro et al., 7-Fairfax et al.

out_mfg_stg_svz_tha_sClusters.metasoft.gz - METASOFT results for sQTLs meta-analysis from MiGA four brain regions (gzip-compressed). Table columns are formatted as follows:

RSID - Id composed by splicing junction coordinates, gene Ensembl ID, and SNP ID separated by underscores for each junction-SNP pair tested in the sQTL study (e.g. chr1_962047_962355_ENSG00000187961.14_1:11008:C:G)

#STUDY - number of studies included in the meta-analysis

PVALUE_FE - P-value of the fixed-effects model (FE) according to METASOFT

BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT

STD_FE - Standard error of BETA_FE

PVALUE_RE - P-value of the random effects model (RE) according to METASOFT

BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT

STD_RE - Standard error of BETA_RE

PVALUE_RE2 - P-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT

STAT1_RE2 - RE2 statistic mean effect part

STAT2_RE2 - RE2 statistic heterogeneity part

PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)

I_SQUARE - I-square heterogeneity statistic

Q - Cochran's Q statistic

PVALUE_Q - Cochran's Q statistic's P-value

TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird

PVALUES_OF_STUDIES(Tab_delimitered) - P-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA

MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA

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