Searching for novel sequence variants associated with cholesterol levels is of particular interest due to the causative role of non-HDL cholesterol levels in cardiovascular disease. Through whole-genome sequencing of 15，220 Icelanders and imputation of the variants identified， we discovered a rare missense variant in (R436H) associating with lower levels of total cholesterol (effect?=?-0.47 standard deviations or -0.55?mmol?L， ?=?4.21?×?10， ?=?150，211). Importantly， R436H also associates with lower levels of non-HDL cholesterol and， consistent with this， protects against coronary artery disease. encodes FXR that regulates bile acid homeostasis， however， we do not detect a significant association between R436H and biological markers of liver function. Transcriptional profiling of hepatocytes carrying R436H shows that it is not a loss-of-function variant. Rather， we observe changes in gene expression compatible with effects on lipids. These findings highlight the role of FXR in regulation of cholesterol levels in humans.