Human osteoclast eQTL 2018-2020

Human osteoclast expression quantitative trait locus (eQTL) study 2018-2020

This is a single cohort eQTL study of 158 human osteoclast-like cell cultures that were differentiated from peripheral blood mononuclear cells.


This dataset was generated as part of an eQTL study of osteoclast-like cells differentiated from peripheral blood mononuclear cells obtained from 158 women attending Sir Charles Gairdner Hospital in Western Australia for a dual-energy X-ray absorptiometry bone mineral density scan. The subjects were aged 30-70 years and all had self-reported European ancestry. Quantitation of gene expression in the osteoclast-like cells was performed using 50 bp single-end RNA-Seq on an Illumina HiSeq 2500, with a total of 15,688 expressed gene transcripts identified. Genotyping was performed using the Illumina Infinium OmniExpress-24 BeadChip array, with imputation performed by the Sanger Imputation Service using the Haplotype Reference Consortium (HRC) release 1.1 reference panel. Any variants with an IMPUTE2 info score <0.4 or minor allele frequency (MAF) <5% were removed from the imputed dataset. After genotype imputation and QC, genotype data was available for 5,373,348 variants in the study sample. The eQTL association analysis was performed using the FastQTL software (implementing quantile normalisation), adjusting for the following covariates: patient age, RNA-Seq batch and 10 genomic principal components. Each variant was tested for association with the expression of any gene with a transcription start site located within a 2 Mb window on either side of the variant.

Data file description

Each file contains the following information:

Variant rsID or chr:position (hg19). Effect allele. Non-effect allele. Gene symbol Distance between the variant and the gene transcription start site. Nominal p-value of association (not adjusted for multiple testing). Normalised effect size on gene expression for the effect allele.


Mullin, B. H., J. Tickner, K. Zhu, J. Kenny, S. Mullin, S. J. Brown, F. Dudbridge, N. J. Pavlos, E. S. Mocarski, J. P. Walsh, J. Xu and S. G. Wilson (2020). "Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts." Genome Biol 21(1): 80

Mullin, B. H., K. Zhu, S. J. Brown, S. Mullin, J. Tickner, N. J. Pavlos, F. Dudbridge, J. Xu, J. P. Walsh and S. G. Wilson (2019). "Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget's disease of bone." Sci Rep 9(1): 1052

Mullin, B. H., K. Zhu, J. Xu, S. J. Brown, S. Mullin, J. Tickner, N. J. Pavlos, F. Dudbridge, J. P. Walsh and S. G. Wilson (2018). "Expression Quantitative Trait Locus Study of Bone Mineral Density GWAS Variants in Human Osteoclasts." J Bone Miner Res 33(6): 1044-1051

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