Here we investigate synthetic association by analyzing if common genetic variation (SNPs and haplotypes thereof) genotyped in the non-coding genomic region of the MC4R locus is related to coding (functional) variants of the MC4R. In the first step, we analyzed the genomic region covering both 3′ SNPs (rs17782313 and rs12970134), the MC4R and SNPs in its 5′ flanking region to extract all evidence for common variation related to obesity at the MC4R locus. Here, MC4R is linked to obesity due to melanocortin 4 receptor deficiency.