Recent advances in single-cell omics allows cellular heterogeneity dissection and regulatory landscape reconstruction with an unprecedented resolution. In this work, we elaborated our effort to improve single cell ATAC sequencing (scATAC-seq) resolution and used single cell RNA sequencing (scRNA-seq) to reveal neutrophils heterogeneity. Comparing to bulk ATAC-seq sequencing, scATAC-seq’s ultra-high missingness remarkably reduces usable reads in each cell type, resulting in broader, fuzzier peak boundary definitions and limiting our ability to pinpoint functional regions and interpret variant impacts precisely. We propose a weakly supervised learning method, scEpiLock, to directly identify core functional regions from coarse peak labels and quantify variant impacts in a cell-type-specific manner. First, scEpiLock uses a multi-label classifier to predict chromatin accessibility via a deep convolutional neural network. Then, its weakly supervised object detection module further refines the peak boundary definition using gradient-weighted class activation mapping (Grad-CAM). Finally, scEpiLock provides cell-type-specific variant impacts within a given peak region. We applied scEpiLock to various scATAC-seq datasets and found that it achieves an area under receiver operating characteristic curve (AUC) of ~0.9 and an area under precision recall (AUPR) above 0.7. Besides, scEpiLock’s object detection condenses coarse peaks to only ⅓ of their original size while still reporting higher conservation scores. In addition, we applied scEpiLock on brain scATAC-seq data and reported several genome-wide association studies (GWAS) variants disrupting regulatory elements around known risk genes for Alzheimer’s disease, demonstrating its potential to provide cell-type-specific biological insights in disease studies. Next, we used scRNA-seq to understand the neutrophils diversity among five different organs. We offered a thorough depiction of the transcriptional profile of neutrophil maturation and function in both their normal condition and in response to tumor. Five neutrophil populations were defined by distinct molecule signatures. Tumor attracted early-stage neutrophils and upregulates several genes like Ifitm1 and Wfdc17. In addition, we identified a systemic expansion of Ifitm1 positive neutrophils near breast cancer, which showed tumor suppression signature. In summary, this study establishes a reference model and scRNA-seq analysis framework for studying neutrophil heterogeneity, development, and impact on disease.