Table 2.

CWAS summary

Genetic variants/conditions/traits	Status	Connections		Beta values		Top-decile β values	P-value effect
		pos	neg	min	max
1q21.1	DEL	1	11	−1.07	0.62	0.44	0.002
	DUP	4	0	−0.62	0.84	0.48	0.002
22q11.2	DEL	4	13	−1.48	1	0.65	<2 × 10−4
	DUP	0	2	−0.78	0.69	0.43	0.04
16p11.2	DEL	124	149	−0.98	1.67	0.57	<2 × 10−4
	DUP	4	3	−1.04	0.55	0.38	0.002
15q11.2	DEL	1	0	−0.29	0.36	0.2	0.01
Idiopathic psychiatric conditions	SZ	221	258	−0.41	0.51	0.30	<2 × 10−4
	BIP	33	24	−0.66	0.65	0.43	<2 × 10−4
	ASD	51	55	−0.26	0.36	0.16	<2 × 10−4
	ADHD	0	0	−0.22	0.22	0.15	<2 × 10−4
Non-psychiatric condition	IBD	0	0	−0.16	0.16	0.11	ns
Polygenic scores	Autism	3	1	−0.02	0.02	0.01	0.04
	SZ	93	115	−0.02	0.04	0.02	<2 × 10−4
	BIP	16	2	−0.02	0.03	0.01	0.002
	MDD	6	21	−0.02	0.03	0.01	0.003
	Cross-Disorder	23	22	−0.02	0.03	0.01	<2 × 10−4
Traits	Fluid intelligence	311	281	−0.04	0.04	0.02	<2 × 10−4
	Neuroticism	208	208	−0.03	0.04	0.02	<2 × 10−4

The number of significantly altered connections (FDR corrected) for each CWAS (n = 19). min-max = minimum-maximum of z-scored beta values; top decile = top decile of beta values; Connection pos = number of positive connections surviving FDR; Connection neg = number of negative connections surviving. DEL = deletion; DUP = duplication; MDD = major depression disorder; Cross Dis = cross-disorder.