Usually, enhancers can activate distal gene expression via interactions with proximal promoters, which might be mediated by various transcription factors. Although such reports have been reported in human as well as several model plants (e.g Arabidopsis), whether and how enhancers regulate gene expression is still lacking in soybean, especially the enhances activities in response to environmental stimuli, such as light, the essential environmental factor for plant development and survival. Since that the ATAC-seq is widely used for identification of the distal cis-regulatory element (e.g. enhancers), in this studies, we firstly adopted this method to identify light responsive the enhancer-like elements in soybean seedlings. Furthermore, through the several molecular experiments, such as Y1H, 3C-qPCR, BiFC etc, we provided clear molecular evidences that the enhancers candidates (E2) form a chromatin loop which mediated by the WRKY and SBP transcription factors to regulate the downstream genes (GS) in response to light. Also, as the important genomic resources, we submitted these ATAC-seq data to the public database DataHub (https://datahub.wildsoydb.org) for further investigation.