Osteoclast-Specific eQTL Results for Osteoporosis Risk Variants

GEnetic Factors for OSteoporosis Consortium (GEFOS) provides osteoclast-specific expression quantitative trait locus summary statistics for 21 genetic loci. The data was generated from a study of 158 osteoclast cell cultures using Illumina OmniExpress-24 BeadChip array genotyping and HiSeq 2500 RNA-Seq. Author Benjamin H. Mullin published the underlying research in papers with PMIDs 32216834, 29473973, and 30705363.

Use Cases

• Identify candidate causal genes for osteoporosis by colocalizing eQTL signals with bone mineral density GWAS hits.
• Investigate cell-type-specific genetic regulation of gene expression in human osteoclasts.
• Prioritize genetic variants for functional follow-up studies based on their association with gene expression in a relevant cell type.

Strengths

• Data is derived from 158 specific osteoclast cell cultures, providing a focused cellular context.
• Analysis was adjusted for covariates including patient age, RNA-Seq batch, and 10 genomic principal components.
• Only variants with a minor allele frequency (MAF) of at least 5% were included, focusing on more common genetic variation.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

GEnetic Factors for OSteoporosis Consortium (GEFOS) website.

Collection Method

Genome-wide array genotyping with imputation using the Haplotype Reference Consortium panel, followed by RNA-Seq and eQTL analysis with FastQTL software.