Finally, Table 3 lists the contribution of the discovered loci to the total genetic variance of the respective traits across the 62 meta-analyses with suitable data available for estimating the variance. Ankylosing spondylitis was the trait with the largest portion of genetic variance explained, as the 7 loci reaching genome-wide significance explained 79% of the variance. This is largely attributed to the effect of rs4349859 in HLA-B with OR=56 and P<10−200. This locus is a well-established risk factor and diagnostic test for the disease. Several other phenotypes had over 20% of their variance explained: Crohn’s disease (71%), rheumatoid arthritis (52% in Europeans and 33% in Asians), multiple sclerosis (49%), ulcerative colitis (39%), type 1 diabetes (36%), and Parkinson’s disease (20%). There was a weak correlation (r=0.28, P=0.03) between the number of discovered/validated SNPs and the proportion of variance explained, e.g. 115 validated SNPs explained less than 7% of the variance of height. Many phenotypes had very low proportions of variance explained. The lowest explained variance was found for ankle-brachial index (only 1 SNP was genome-wide significant and explained <0.1% of
