Our top genome-wide finding involved three SNPs (rs7031417, rs17053864, rs7019589) at pseudogene LOC100129340 (mitofusin-1-like). Very little is known regarding this pseudogene, which was only added in the most recent, hg19, gene track (thus, its absence in the regional plot). However, variants within LOC100129340 were found to be associated with adult human height in a large GWAS meta-analysis (Gudbjartsson et al., 2008). Also, one of the genome-wide significant hits fell within exon 4 of the pseudogene. Given that pseudogenes, by definition, lack protein-coding function, the prior probability of this locus being a true discovery is somewhat diminished. However, considering: a) the association signal is in a transcribed sequence, b) pseudogene transcripts have demonstrated trans-regulation of homologous coding genes (Hirotsune et al., 2003) and c) endogenous siRNA are sometimes derived from pseudogene transcription (Tam et al., 2008), it would be rash to dismiss this result as a false discovery.
