TABLE VII.

Probability of a real gene given no-change in significance of an associated SNP after fine mapping, for a disease allele frequency of 0.2

Genetic model (H1)		Ten SNPs somewhere in the genome P(H1)=0.00166			One SNP somewhere under a 20Mb wide linkage peak P(H1)=0.025			One SNP immediately under the peak P(H1)=0.667
GRRhom	GRRhet	P(H1|i,s)	P(H1|s)	PC (%)	P(H1|I,s)	P(H1|s)	PC (%)	P(H1|i,s)	P(H1|s)	PC (%)
1.5	1.5	0.00784	0.01379	−43	0.108	0.177	−39	0.905	0.944	−4.1
1.5	1.0	0.00182	0.00198	−8	0.027	0.030	−8	0.686	0.704	−2.6
1.5	1.25	0.00487	0.00699	−30	0.07	0.098	−28	0.855	0.894	−4.4
2.0	2.0	0.00851	0.01959	−57	0.117	0.235	−50	0.912	0.96	−5.0
2.0	1.0	0.00249	0.00310	−20	0.037	0.046	−19	0.75	0.789	−4.9
2.0	1.5	0.00881	0.01706	−48	0.12	0.211	−43	0.914	0.954	−4.2
3.0	3.0	0.00895	0.02039	−56	0.122	0.243	−50	0.916	0.962	−4.8
3.0	1.0	0.00423	0.00574	−26	0.061	0.082	−25	0.836	0.874	−4.3
3.0	2.0	0.00939	0.01994	−53	0.127	0.238	−47	0.919	0.961	−4.3

P(H₁) – prior probability of a genetic effect.

P(H₁|s) – posterior probability of a genetic effect given a significant primary analysis signal.

PC (%) – proportional change in posterior probability of a genetic effect, given by 100[P(H₁|i,s)–P(H₁|s)]/P(H₁|s).