Table III.

Permutation‐Based Enrichment Analysis for GWAS Top‐Associated Genetic Loci

	GWAS dataset	Permuted datasets
Outcome	Nobs	Nexc/Nperm	P emp	50th PCTL		Nobs‐50th PCTL	5th PCTL	Nobs‐5th PCTL
IQ	391	11/1000	0.011	343		48	378	13
CPT	338	60/100	ns	342		‐	375	‐
CPT‐RT	349	36/100	ns	340		9	375	‐
VNB	418	0/3000	<0.001	344		74	379	39
VNB‐RT	323	84/100	ns	347		‐	378	‐
SNB	370	7/100	ns	343		27	373	‐
SNB‐RT	354	33/100	ns	345		10	383	‐
ERT	357	25/100	ns	343		14	382	‐
ART	381	35/1000	0.035	345		36	378	3
ACV	448	0/3000	<0.001	352		96	387	61
SPEM	335	67/100	ns	345		‐	382	‐

N_obs, number of observed loci at GWAS P < 0.001.

N_exc, number of permutation where the number of loci at P < 0.001 exceeded N_obs.

N_perm, number of permutations performed.

P _emp, empirical P‐value. Significant enrichment at P <0.05 is shown in bold.

PCTL, percentile, for example 5th PCTL is the number of loci with P < 0.001 in 5% of permutations.ns, not significant (P _emp > 0.05).