Multivariate genome-wide association study models to improve prediction of Crohn’s disease risk and identification of potential novel variants

•Multivariate models allow ranking variants, according to their contribution to the disease-risk prediction.•LDpred performed better to predict CD-risk, compared with other multivariate and the common polygenic risk score (PRS) analysis.•The LDpred model without imputation was the best model to predict CD risk (AUROC = 0.667 ± 0.024) in the UKIBDGC dataset.•An unnoticed region was identified, within chr 6 (SNP rs4945943) close to gene MARCKS, likely to contribute to CD risk.