Table 3.

Enrichment of association signals in 20 target gene sets

	Dispersion				Burden
Name	GeneSet	EnhancerSet	Enhanced GeneSet	GeneSet	EnhancerSet	Enhanced GeneSet
FMRP_targets_Darnell2011	5.0E−05	0.0016	2.2E−06	0.0057	2.6E−04	6.2E−04
ASD_coexpression_networks_Willsey2013	0.4368	0.8772	0.3939	7.6E−05	0.0013	2.5E−05
Constrained_PLIScoreOver0.9	2.2E-04	0.1319	1.3E−04	1.9E−04	7.0E−04	4.7E−05
FXR2_wt_binding_sites	0.0083	0.0315	0.0012	0.0023	9.9E−05	2.6E−04
FMR1_iso1_wt_binding_sites	0.0254	0.0225	0.0100	0.0133	0.0014	0.0021
FMR1_iso7_I304N_binding_sites	0.0485	0.0088	0.0162	0.0230	4.6E−04	0.0055
FMR1_iso7_wt_binding_sites	0.2504	0.1216	0.1942	0.0226	0.0082	0.0055
Processed_Transcript_GencodeV19	0.0257	—	0.0257	0.0114	—	0.0114
FMR1_iso1_I304N_binding_sites	0.2328	0.0640	0.1521	0.1010	3.3E−04	0.0237
regulatory_elements_neuro	0.0269	—	0.0269	0.3980	—	0.3980
FXR1_wt_binding_sites	0.0611	0.1849	0.0841	0.1087	0.0381	0.1104
BrainExpressed_Kang2011	0.6152	0.0030	0.2729	0.5306	0.0169	0.3241
Protein_Coding_GencodeV19	0.7413	4.4E−04	0.3192	0.4560	0.0363	0.3496
CHD8_targets_Cotney2015_Sugathan2014	0.3743	0.0080	0.3512	0.9345	0.2153	0.9074
Antisense_GencodeV19	0.4770	—	0.4770	0.4183	—	0.4183
lincRNA_GencodeV19	0.9507	—	0.9507	0.4613	—	0.4613
ASD_risk_genes_TADA_FDR0.3	0.7783	0.1752	0.6973	0.4770	0.8620	0.4671
PSD_Genes2Cognition	0.9944	0.0165	0.8704	0.6989	4.6E−04	0.4879
PseudoGencodeV19	1.0000	—	1.0000	0.5864	—	0.5864
Developmental_delay_DDD	0.7380	0.4580	0.6310	0.9987	0.4166	0.9908

For each gene set, we consider three related sets: the original gene set, enhancers predicted to interact with genes in the set, and an enhanced gene set containing both genes and the predicted enhancers. p-values from enrichment analyses are reported; those smaller than Bonferroni threshold = 0.05/20 = 0.0025 are bolded