README file for the xQTLServe_mQTL_nominally_significant_hg19 dataset I. Description of the dataset -------------------------------- Data source: xQTLServe Data source URL: https://mostafavilab.stat.ubc.ca/xQTLServe/ Genome build: hg19 File format: bed bed6+14 qtl, bgzip-compressed and tabix-indexed Contents: mQTL SNP nominally significant associations Dataset URL: https://tf.lisanwanglab.org/GADB/FILER2/Annotationtracks/xQTLServe/mQTL/nominally_significant/bed3plus17_qtl/hg19/ Acknowledgements: https://tf.lisanwanglab.org/GADB/FILER2/acknowledgements/xQTLServe.html II. Dataset version number -------------------------------- v2_0529_2026 III. Files in the dataset -------------------------------- See MANIFEST for the complete file list. Summary: - Files: 1 *.bed.gz files - Auxiliary indexes: giggle_index/ IV. Contributors -------------------------------- Jeffrey Cifello Prabhakaran Gangadharan Luke Carter Pavel P. Kuksa Fanny Leung V. Workflow description -------------------------------- Files were processed and standardized using FILER data integration and harmonization pipeline (hipFG). VI. Input files and Resources -------------------------------- Original files were obtained from https://mostafavilab.stat.ubc.ca/xQTLServe/. VII. File Contents -------------------------------- 1. Example annotation file: formatted_output_xQTLServe_combined_mQTLs_nominally_significant.bed.gz File schema: fieldName sqlType fieldDescription chrom string Reference sequence chromosome chromStart uint Start position in chromosome, 0-based coordinate system chromEnd uint End position in chromosome name string Identifier for the genetic variant score uint p-value score indicating the significance of the association between the variant and the gene expression. strand char[1] Strand of the target gene relative to the reference genome (+ for forward, - for reverse) ref lstring The reference allele at the given position on the chromosome alt lstring The alternate allele(s) that differ from the reference at the specified position target_gene_symbol lstring Gene symbol for the gene affected by the variant target_ensembl_id lstring Ensembl gene ID of the target gene target string Alternative target gene identifier z_score_non_ref float Z-score for the effect of the non-reference allele beta_non_ref float Effect size of the non-reference allele on gene expression beta_se_non_ref float Standard error of the effect size for the non-reference allele FDR string False Discovery Rate non_ref_af string Allele frequency of the non-reference allele qtl_dist_to_target int Distance between the variant and the target gene’s start or end position QC_info lstring Quality control information target_info lstring Additional metadata about the target gene user_input lstring Additional user-provided annotations 2. Example tabix index file: formatted_output_xQTLServe_combined_mQTLs_nominally_significant.bed.gz.tbi The annotation track is tabix-indexed to allow efficient retrieval of annotations by chromosome and position. --------------------------------- Generated from: - Metadata: https://tf.lisanwanglab.org/FILER2/metadata/filer2.latest.hg19.template - File schemas: https://tf.lisanwanglab.org/FILER2/metadata/filer2.schemas.latest.tsv - README template: https://tf.lisanwanglab.org/GADB/metadata/filer.dataset.readme.template - Generation date: 06/05/2026