Advances in next-generation sequencing technology have made it possible to comprehensively interrogate the entire spectrum of genomic variations including rare variants. They may help capture the remaining genetic heritability which has not been fully explained by previous genome-wide association studies. Here we performed a gene-based genome-wide scan to identify hypertension susceptibility loci in analysis of a whole genome sequencing cohort of 103 unrelated individuals. We found that collapsing singletons may boost signals for associating rare variants and identified SETX statistically significant by a genome-wide gene-based threshold (p value <5.0 × 10(-6)). The function of SETX in hypertension may be worthy of further investigation.