Table 3.

Credible Sets of Causal SNPs at Known Associated Loci

Phenotype	No. of Loci	Total SNPs	Flat Prior	Coding Prior	Main Functional Priors	Main and Enhancer Priors
RA	5	8,393	69	69	26	26
T2D	13	24,799	101	90	84	83
CAD	16	27,685	112	112	90	86
CAD (metabo-chip)	34	7,498	325	325	264	260
PGC2	146	582,401	5,696	5,660	4,756	not available

For each trait, genome-wide-significant loci from meta-analysis association statistics were reduced to 95% credible sets with and without functional priors. The right-most four columns describe the number of SNPs in the credible set obtained from each prior type. “Flat prior” corresponds to standard analysis with no functional information. “Coding prior” uses only enrichment at coding variants. “Main functional priors” include all six priors from the main functional analysis. “Main and enhancer priors” include all six main priors and the enhancer-DHS prior.