TABLE VI.

Probability of a real gene given an increase in significance (any order of magnitude) of an associated single SNP following fine-mapping, for a disease allele frequency of 0.2, stratified by r² between the disease SNP and the primary analysis signal

Genetic model		Ten genes in the genome P(H1)=0.00166						One gene under a 20-Mb linkage peak (H1)=0.025
		r2<0.5		r2≥0.5		r2<0.5		r2<0.5		r2≥0.5		r2≥0.8
GRRhom	GRRhet	P(H1|i,s)	PC (%)	P(H1|i,s)	PC (%)	P(H1|i,s)	PC (%)	P(H1|i,s)	PC (%)	P(H1|i,s)	PC (%)	P(H1|i,s)	PC (%)
1.5	1.5	0.02410	96	0.02793	92	0.02513	74	0.275	71	0.306	66	0.284	54
1.5	1.0	0.00220	13	0.00413	68	0.00345	48	0.033	13	0.060	65	0.051	46
1.5	1.25	0.00929	42	0.01421	90	0.01367	84	0.126	37	0.181	74	0.176	70
2.0	2.0	0.04742	156	0.04140	107	0.03746	86	0.434	93	0.399	67	0.374	56
2.0	1.0	0.00390	27	0.00603	90	0.00546	71	0.057	25	0.085	83	0.078	66
2.0	1.5	0.03584	130	0.03419	93	0.03100	75	0.364	86	0.353	63	0.330	52
3.0	3.0	0.05505	173	0.04075	99	0.03612	76	0.473	96	0.395	62	0.366	50
3.0	1.0	0.00781	38	0.01056	81	0.01001	72	0.108	34	0.141	70	0.135	63
3.0	2.0	0.05278	169	0.03885	94	0.03382	69	0.462	96	0.383	60	0.350	46

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).