Exon-level ciseQTL Analysis of RSPO3

The TwinsUK samples were genotyped on a combination of Illumina chips, namely the HumanHap300, HumanHap610Q, 1M-Duo and 1.2MDuo Illumina arrays. Samples were imputed using the Haplotype Reference Consortium (HRC) reference panel (http://www.haplotype-reference-consortium.org), using Minimac 3 on the Michigan Imputation Server (https://imputationserver.sph.umich.edu). Genotype data were filtered to exclude SNVs with HWE P < 1 × 10⁻⁶, imputation R² < 0.8, or a minor allele frequency (MAF) < 0.01. RNA-seq expression data from subcutaneous adipose tissue were available for 766 twins. RNA-seq data were generated, quantified and normalised^{68 (link)}. Expression data were adjusted for family structure (family and zygosity) and 50 PEER factors using mixed effects models fitted using the lmer function from the lme4 package in R, and expression residuals used for ciseQTL analysis. Exon-level ciseQTL analysis at the RSPO3 gene was conducted within a 2 Mb window surrounding the transcription start site using the MatrixeQTL package in R version 3.5.0, which employs a standard additive linear model, with BMI, age and RNA extraction batch included as covariates.