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A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (Peng et al., 2011). The paper looked at 59 studies and concluded that, "FTO may represent a low-penetrance susceptible gene for obesity risk", although the association was weaker (or non-existent) for some ethnic groups.

Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?

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I was always wondering whether detecting such SNPs links to diseases (risk) is of significance. Sometimes, I think biology is so complex, even for diagnosis SNPs don't help very much. I am just chattering. – LifeWorks May 8 '12 at 22:59
I think there are some statistical issues with this - such as multiple testing and family-wise error, but most of the studies in the meta-analysis I linked to seem to be quite solid and found odds ratios with confidence intervals comfortably above 1. Clearly it is well known that obesity etiology is multi-factorial and genetics plays a relatively smaller part (compared to the environment), but the evidence does seem clear that there are some genetic components, and gene-environment interactions are also likely. – Robert Long May 9 '12 at 6:24
up vote 6 down vote accepted

MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see Thorleifsson et al. (2009), Elks et al. (2010) and Willer (2009)

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Yes, FTO is the strongest thus far in the populations thus far tested. If Asians or African populations were to be tested as deeply, as often as European populations, other genes certainly may be added to the list. – Larry_Parnell May 11 '12 at 13:56

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