CAGE and txrevise promoter usage QTL summary statistics

This dataset contains promoter usage QTL summary statistics obtained using QTLmap. QTLmap_summary_CAGE.txt contains summary statistics for CAGE, QTLmap_summary_txrevise-25.txt for regular txrevise and QTLmap_summary_txrevise-supplemented-20.txt for txrevise with the new generated annotations.

This dataset contains the promoter annotations obtained with CAGE as part of the FANTOM5 project, cleaned and reformatted using this code for the purpose of QTL mapping, that were used to obtain the aforementioned summary statistics. They can be found in Cleaned_FANTOM5_promoter_annotations.tsv.

QTL summary statistics column descriptions:

molecular_trait_object_id - gene

molecular_trait_id - top promoter for the gene

n_traits - how many promoters were tested for the gene

n_variants - how many genetic variants were tested for the promoter

variant - top genetic variant for the promoter

chromosome - chromosome

position - promoter's top genetic variant start position

pvalue - nominal p-value of the association between the promoter and genetic variant

beta - the fitted linear model's regression coefficent

p_perm - empirical p-value calculated using permutations

p_beta - estimated empirical p-value based on the beta distribution, this is the recommended p-value column