Several studies have shown that using genetic data from commensal chicken as proxy can provide key information for inferring prehistoric human migration patterns. Previous studies utilized both short and genomic-scale DNA sequences to examine and answer questions about past human mobility. Although genetic sequences are more commonly used, studies using genomic-scale data, albeit more complex to obtain, could provide information that shorter DNA sequences cannot yield. In addition, methods for extracting and analyzing genomic-scale data are becoming more accessible than before, and publications of studies using genomic-scale data are rapidly increasing today. In this study, the advantage of using genomic-scale data of chickens as proxy for investigating human migration patterns lies on the more refined information generated for population structure analysis and the examination of loci under selection. Here, we analyzed nuclear SNP dataset from 51 domestic and wild chicken samples representing seven populations in the Asia-Pacific as proxy to study human migration in this region, through a set of methods and while acknowledging for ascertainment bias. We filtered the SNP array through LD-based pruning, reducing the original 580,961 SNPs to 132,468. After testing for selection using the FST-outlier approach, a total of 132,418 neutral loci were used for population structure analyses, while the associated genes for the 50 loci identified as outliers were determined. Our results using Principal Component Analysis and ADMIXTURE exhibited distinct genomic differences between commercial chickens and wild red jungle fowls, and among domestic chickens across Mainland Asia, the Philippines, and the Pacific. This study contributes to the discussion on chicken translocation and the Austronesian migration in the Asia-Pacific region and shows how the genomic-scale datasets serve as proxy data for human migration research.