To indicate the importance of PAS-SNPs in the development of obesity and to promote this field of research, the aims of the present study were (1) to identify PAS-SNPs in the divergent mouse models for body fat percentage, (2) to analyse the biological processes of genes with PAS-SNPs using bioinformatics databases, (3) to identify disease-, obesity- and APA-related genes with PAS-SNPs and (4) to identify PAS-SNPs within candidate genes with potential functional impact on their expression. This evidence concerns the gene ENPEP and obesity due to melanocortin 4 receptor deficiency.