Obesity is accompanied by low-grade systemic inflammation that etiologically contributes to obesity-induced cardiovascular disease (CVD). Growing evidence supports that neutrophil, the most abundant type of leukocytes in human, is most likely to be the target peripheral leukocyte subtype initiating the inflammatory cascade in obesity. However, few studies have systematically assessed the genome wide changes in neutrophils associated with obesity. In this study, a hypothesis-free OMIC approach (i.e. the discovery phase) and a target approach (i.e. the validation phase) were used to identify obesity related neutrophil activation markers and their roles on CVD risks. In the discovery phase, genome wide DNA methylation, RNA-sequencing and quantitative proteomics were obtained from purified neutrophils (12 obese
vs
. 12 lean). In the validation phase, gene expression levels of the promising genes from the OMIC platforms were measured in 81 obese cases
vs
. 83 lean controls, and the association between the expression levels and CVD risks were evaluated. Significant difference was found for one gene, alkaline phosphatase, liver/bone/kidney (
ALPL
), across 3 OMIC platforms. In the validation phase, the gene expression levels of
ALPL
in leukocytes were significantly higher in obese compared with lean subjects (p < 0.05). Within the obese population, we observed that
ALPL
expression level showed significantly positive association with CVD risk factors (p < 0.05) including systolic blood pressure, diastolic blood pressure, mean arterial pressure, carotid intima–media thickness and borderline significance with fasting insulin (p = 0.08). This study identified one novel marker
ALPL
of neutrophil activation in response to obesity and provided evidence that obesity induced change in
ALPL
expression was associated with CVD risk factors.