Skeletal muscle bulk eQTL meta-analysis of GTEx + FUSION (Wilson et al. AJHG in revision 2025)
Skeletal muscle bulk eQTL meta-analysis summary statistics of GTEx + FUSION (Wilson et al. AJHG in revision 2025)
Below are the links for:
- Supplemental tables 2-3 with the list of eQTL signals (lead variants per gene per signal) (hg38 and hg19)
- Full marginal eQTL summary statistics (hg38 and hg19)
- Conditionally isolated eQTL summary statistics for each signal (hg38 and hg19)
| eQTL lead variants (Tables S2-3): | |
| Column label | Description |
| Gene symbol | Gene symbol |
| Gene | Ensembl ID for GENCODE v19 |
| Chr | Chromosome |
| Pos | Position |
| EA | Effect allele |
| NEA | Non-effect allele |
| EAF | Effect allele frequency |
| Beta | Variant to gene effect for the joint model with all signals for the effect allele |
| SE | Standard error |
| Pvalue_joint | P-value of the joint model including all of the eQTL signals that pass the 1e-5 stepwise threshold |
| Studies (1=FUSION, 2=GTEx) | Studies contributing to meta-analysis of this gene |
| Signal number for eGene (Current:Total) | Variant’s signal number out of all signals for the eGene (for instance, 2:03 means this was the second signal identified out of three for this eGene) |
| BH-adjusted p-value | FDR-adjusted p-value accounting for independent tests within this eGene |
| Files for download: | |
| Description | Table S2: Lead variants from skeletal muscle eQTL meta-analysis (hg38) |
| Filename | Muscle_eQTL_MetaAnalysis_SuppTable2_LeadVariants_hg38.txt |
| Size | 1.5 MB |
| Date | 2025-08-05 |
| Description | Table S3: Lead variants from skeletal muscle eQTL meta-analysis (hg19) |
| Filename | Muscle_eQTL_MetaAnalysis_SuppTable3_LeadVariants_hg19.txt |
| Size | 1.6 MB |
| Date | 2025-08-05 |
| Marginal eQTL summary stats: | |
| Column label | Description |
| gene | Ensembl ID for GENCODE v19 |
| SNP_hg* | Marker name for the SNP with the alleles formatted alphabetically (chr_pos_A1_A2) |
| chr | Chromosome |
| pos | Position |
| EA | Effect allele |
| NEA | Non-effect allele |
| beta | Marginal variant to gene effect for the effect allele |
| se | Standard error |
| pval | Marginal p-value |
| studies | Studies contributing to meta-analysis of this gene (1=FUSION, 2=GTEx) |
| Files for download: | |
| Description | Marginal eQTL full summary statistics (hg38) – all results by chromosome |
| Filename | Muscle_eQTL_MetaAnalysis_fullMarginalSumStats_hg38.tar.gz |
| Size | 2.7 GB |
| Date | 2025-08-05 |
| Description | Marginal eQTL full summary statistics (hg19) – all results by chromosome |
| Filename | Muscle_eQTL_MetaAnalysis_fullMarginalSumStats_hg19.tar.gz |
| Size | 4.0 GB |
| Date | 2025-08-05 |
| Conditional eQTL summary stats: | |
| Column Label | Description |
| gene | Ensembl ID for gene GENCODE v19 |
| SNP_hg* | Marker name for the SNP with the alleles formatted alphabetically (chr_pos_A1_A2) |
| chr | Chromosome |
| pos | Position |
| EA | Effect allele |
| NEA | Non-effect allele |
| beta | Variant to gene effect for the joint model with all signals for the effect allele; if the gene has only one signal, the marginal beta is provided |
| se | Standard error |
| pval | If the gene has more than one signal, the conditional joint p-value is provided; otherwise, the marginal p-value is provided |
| lead_SNP_hg* | If the gene has more than one signal, this is the lead variant of the signal for which conditional statistics are provided; if the gene has only one signal, this is “NA” |
| studies | Studies contributing to meta-analysis of this gene (1=FUSION, 2=GTEx) |
| SNP_N | SNP sample size |
| gene_N | Gene sample size |
| Files for download: | |
| Description | Conditionally isolated eQTL summary statistics for each signal (hg38) – all results by chromosome |
| Filename | Muscle_eQTL_MetaAnalysis_fullAB1SumStats_hg38.tar.gz |
| Size | 3.0 GB |
| Date | 2025-08-05 |
| Description | Conditionally isolated eQTL summary statistics for each signal (hg19) – all results by chromosome |
| Filename | Muscle_eQTL_MetaAnalysis_fullAB1SumStats_hg19.tar.gz |
| Size | 4.5 GB |
| Date | 2025-08-05 |