Table 1.

The performance of fastPAINTOR is largely sustained when the assumption of shared causal variants across traits is violated

Method	Proportion of causals identified	SNPs selected (s.e.)
Trait 1	0.96	46.01 (0.27)
Trait 2	0.96	45.54 (0.27)
Differing causals	0.86	28.42 (0.22)
Same causals	0.97	26.00 (0.17)

As compared with fine-mapping single traits independently, the reduction in the 95% credible set size is sustained while still capturing a large proportion of the causal variants. We define an 95% confidence set as the number of SNPs we need to select in order to accumulate 95% of the total posterior probability mass per locus.