Forensic characteristics and phylogenetic analysis of the Chinese Han population from Chongqing Municipality, Southwest China

•Genetic polymorphisms of 27 Y-STR loci and predicted Y-SNP markers in the Chongqing Han group were investigated.•Pairwise Rst values were evaluated in AMOVA analysis and visualized through MDS.•Network analysis showed that Chongqing Han was closely related other Han group and some southern populations. Chongqing Han is an important southern Han group, but investigations on its paternal genetic structure are still limited. Here, we analyzed the forensic and phylogenetic characteristics of the Chongqing Han population based on 27 Y-STR and predicted Y-SNP markers. Based on AMOVA, haplogroup distribution and network analysis, we explored the genetic relationship between Chongqing Han, other Chinese groups and some southern indigenous groups (speaking Kra-Dai, Austronesian, etc).