e/sQTL summary statistics from “The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force” (Wang et al 2022)


Column descriptions for `taskforce_rna_releasedata_cis_eqtls.tsv.gz`:
variant_id_hg19: chr:pos:ref:alt in hg19
variant_id_hg38: chr:pos:ref:alt in hg38
rsid: rsid based on dbSNP release 155, hg38
gene_id: Ensembl Gene ID
tss_distance: Distance from the variant to the transcription starting site (TSS)
ma_samples: Number of samples with minor allele in the study sample (Japan COVID-19 Task Force, n=465)
ma_count: Number of minor alleles
maf: Minor allele frequency
pval_nominal: Nominal eQTL p-value calculated from fastQTL
slope: Effect size of the alternative allele
slope_se: Effect size standard error
pip_fm: Posterior inclusion probability (PIP) from FINEMAP
pip_susie: PIP from SuSiE
ref_is_minor: True if the reference allele is the minor allele in the study sample 

 
Column descriptions for `taskforce_rna_releasedata_cis_sqtls.tsv.gz`:
variant_id_hg19: chr:pos:ref:alt in hg19
variant_id_hg38: chr:pos:ref:alt in hg38
rsid: rsid based on dbSNP release 155, hg38
gene_id: Ensembl Gene ID
cluster_id: Cluster ID defined by Leafcutter
tss_distance: Distance from the variant to the transcription starting site (TSS)
ma_samples: Number of samples with minor allele in the study sample (Japan COVID-19 Task Force, n=465)
ma_count: Number of minor alleles
maf: Minor allele frequency
pval_nominal: Nominal eQTL p-value calculated from fastQTL
slope: Effect size of the alternative allele
slope_se: Effect size standard error
pip_fm: Posterior inclusion probability (PIP) from FINEMAP
pip_susie: PIP from SuSiE
ref_is_minor: True if the reference allele is the minor allele in the study sample

Columns description for `taskforce_rna_releasedata_trans_eqtls.tsv.gz`:
variant_id_hg19: chr:pos:ref:alt in hg19
variant_id_hg38: chr:pos:ref:alt in hg38
rsid: rsid based on dbSNP release 155, hg38
phenotype_id: Ensembl Gene ID
af: Alternative allele frequency
pval: Nominal eQTL p-value calculated from tensorQTL
b: Effect size of the alternative allele
b_se: Effect size standard error

(We preserved the column names from tensorQTL output, resulting in minor differences in the nomenclature compared to the cis-e/sQTL files, which used fastQTL.)


Other notes:
- Only the variant-gene (or intron cluster) pairs with p<0.05 are included in the cis-e/sQTL files, and those with p<5.0*10**-8 are in the trans-eQTL file
- The cis-e/sQTL data are sorted by variant_id_hg38 and tss_distance, ascending order. 
The trans-eQTL data is sorted by variant_id_hg38 and phenotype_id.
(They not necessarily correspond to genomic position order: e.g. chr10 comes earlier than chr2, based on alphabetical order)
- PIPs are calculated only when the minimum p-value for the variant-gene (or variant-intron cluster) is lower than 5.0*10**-8
- We note that there are a very small number of variant-genes with PIP>>0 but are not included due to p>0.05.