Osteoclast-specific eQTL results for osteoporosis risk variants (co-localised loci)

This dataset contains osteoclast-specific expression quantitative trait locus (eQTL) summary statistics for 21 genetic loci demonstrating co-localisation with estimated bone mineral density (eBMD) genome-wide association study (GWAS) association signals from Morris et al. (PMID 30598549). The data is provided in a single .xlsx file. The complete osteoclast eQTL dataset is publicly available on the GEnetic Factors for OSteoporosis Consortium (GEFOS) website (http://www.gefos.org/?q=content/human-osteoclast-eqtl-2018-2020).<br> The eQTL results were generated from a study of 158 osteoclast cell cultures (PMID 32216834, 29473973, 30705363). Genome-wide array genotyping was performed on genomic DNA samples from the study participants using the Illumina Infinium OmniExpress-24 BeadChip array, with imputation performed using the Haplotype Reference Consortium (HRC) release 1.1 reference panel. Transcriptome-wide quantitation of gene expression was performed on the osteoclast RNA samples using 50 bp single-end RNA-Seq on an Illumina HiSeq 2500. Trimmed mean of M-values (TMM) normalisation and correction for total read count by conversion to counts per million (CPM) was performed on the gene expression data using the edgeR package. The eQTL analysis was performed on the TMM-normalised CPM gene expression values using the FastQTL software, implementing quantile normalisation. Only variants with a MAF≥5% were included in the analysis, which was adjusted for the covariates patient age, RNA-Seq batch and 10 genomic principal components.