Genome-wide association studies (GWAS) are a powerful tool for revealing genes associated with common human obesity. New loci associated with obesity have recently been reported, but their function and metabolic implications remain to be elucidated. In order to begin identifying the role of some of these obesity-related loci, the closest genes to the polymorphism of each locus were selected and their expression was compared in the hypothalamus, adipose tissue, liver, soleus muscle, and extensor digitorum longus muscle (EDL) of Long-Evans rats maintained on chow or a high-fat diet (HFD) for 6 weeks. From a total of 19 genes analyzed, seven genes (ETV5, FTO, GNPDA2, KCTD15, TMEM18, MC4R, and SH2B1) were down-regulated in the hypothalamus of HFD compared to chow-fed rats. In adipose tissue of rats fed on HFD, the mRNA levels of BCDIN3, KCTD15, and SULT1A1 were down-regulated, whereas those of MTCH2, PTER, and TUFM were up-regulated. In the liver, three genes were up-regulated (PTER, SULT1A1, and TUFM) in HFD relative to chow-fed rats, and TMEM18 was down-regulated. Finally, in soleus muscle of HFD-fed rats, BCDIN3, BDNF, and TMEM18 were down-regulated, and in the EDL muscle SH2B1 and TUFM were up-regulated. mRNA levels in the hypothalamus were compared between fed and fasted states, and only KCTD15 was down-regulated during fasting when fed a chow diet. In conclusion, novel genes found to be associated with obesity are regulated by a HFD and the mRNA levels of KCTD15 is dependent on the nutritional status. These results suggest a potential role of these genes in the regulation of energy balance.