Colocalization of corneal resistance factor GWAS loci with GTEx e/sQTLs

Data files needed for running codes in https://github.com/xinyixinyijiang/CRF_GTExv8_KC Files: /crf/FINEMAP_credible_sets.tsv: Fine-mapping results for CRF GWAS Loci using FINEMAP. Souce: published in (Jiang et al, 2020) /dapg/*: Input files required for DAP-G for fine-mapping CRF GWAS loci /gtex/: eqtl/ or sqtl/ annotation files in VCF format, required for running colocalisation using fastENLOC containing fine-mapping results of GTEx cis-eQTL and cis-sQTL respectively, consolidated using data shared in (Barbera et.al, 2021). gencode.v26.GRCh38.genes.bed: Used gencode gene annotation file; downloaded from GTEx gtextissue_samplesizes.tsv: Donor sample sizes for GTEx v8 tissues; downloded from GTEx intronref.tsv.gz: Mapping of GTEx Intron ID to tissues and genes; reformated using files downloaded from GTEx rsid_gtexsnpid_ref.gz: Mapping of CRF GWAS variant rsIDs to GTEx variants IDs /keratoconus/: fastenloc/: input files for running colocalisation of CRF-keratoconus GWAS loci using fastENLOC polyfun/: input files for running polyfun for generating variant level priors for fine-mapping Reference: Jiang, X., Dellepiane, N., Pairo-Castineira, E. et al. Fine-mapping and cell-specific enrichment at corneal resistance factor loci prioritize candidate causal regulatory variants. Commun Biol 3, 762 (2020). https://doi.org/10.1038/s42003-020-01497-w Barbeira, A.N., Bonazzola, R., Gamazon, E.R. et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol 22, 49 (2021). https://doi.org/10.1186/s13059-020-02252-4

Jiang, X., Boutin, T., & Vitart, V. (2024). Colocalization of corneal resistance factor GWAS loci with GTEx e/sQTLs. Zenodo. https://doi.org/10.5281/zenodo.13175662