Table 2.

Median flashfm running time (with second and third quartiles), in seconds.

Number of Traits	250-SNP Region (67 kb)	500-SNP Region (144 kb)	1000-SNP Region (312 kb)
2	2 (1, 7)	5 (2, 15)	5 (1, 16)
3	13 (5, 33)	15 (8, 40)	16 (5, 59)
4	435 (49, 2173)	583 (116, 1790)	168 (32, 740)

Flashfm was run using cpp = 0.99 and single-trait fine-mapping results from JAM, using the extended version (JAMexpandedCor.multi) in the flashfm package. Median time was measured over 100 replications in simulations of 2, 3, and 4 traits having correlation 0.4 and sample size 5000. The regions were subsets of the CTLA4 region 2q-204446258-204816382 (GRCh37/hg19).