Table 1.

Burden results for most significant annotation categories from CWAS.

Variant type	Most significant categories within level of analysis	Variants per child (adjusted)	Relative risk	p-value uncorrected	Number of comparisons	p-value corrected
Cases – lowest p-value per cluster in CWAS for top five clusters
De novo indels	Conserved indels near protein coding genes within chromatin state 5 (Weak transcription) regions (Cluster 72)	0.05	2.93	0.0002	4,123	0.66
De novo SNVs	Conserved coding SNVs within post synaptic density genes (Cluster 91)	0.06	2.63	0.0002	4,123	0.82
De novo indels	Conserved intronic indels within chromatin state 15 (Quiescent) regions (Cluster 107)	0.03	5.00	0.0002	4,123	0.91
De novo SNVs	Intergenic SNVs near lincRNAs underlying H3K36me3 (Elongating) peaks (Cluster 58)	4.69	1.11	0.0003	4,123	1.00
De novo SNVs and indels	Conserved coding variants in post synaptic density genes within chromatin state 6 (Genic enhancer) regions (Cluster 23)	0.01	Inf	0.0005	4,123	1.00
Controls – lowest p-value per cluster in CWAS for top five clusters
De novo SNVs	Noncoding SNVs near constrained genes within chromatin state 6 (Genic enhancer) regions (Cluster 175)	0.47	1.36	0.0002	4,123	0.70
De novo SNVs	Intergenic SNVs near pseudogenes underlying H3K9me3 (Constitutive repression) peaks (Cluster 199)	0.41	1.44	0.0002	4,123	0.78
De novo SNVs	Intronic SNVs in constrained genes within chromatin state 5 (Weak transcription) regions (Cluster 75)	6.04	1.09	0.0002	4,123	0.78
De novo SNVs	Noncoding SNVs near constrained genes within chromatin state 5 (Weak transcription) regions (Cluster 20)	7.10	1.07	0.001	4,123	1.00
De novo SNVs and indels	Intergenic variants near genes co-expressed in midfetal brain within chromatin state 5 (Weak transcription) regions (Cluster 121)	0.08	1.86	0.004	4,123	1.00

De novo SNVs and indels from n=519 cases and n=519 controls were compared using a case-control label-swapping permutation analysis as described in Results. P-values were Bonferroni-corrected for 4,123 effective tests.