Table 1. Top 20 diseases whose associated CRs are predicted to affect TAD.

CR ID	Disease Name	CR Type	CR length	Gene	PubMed ID	SI Score (hESC)	FDR (SI score)
145620	Cleft palate	Deletion	3630934	CRYBB2	20466091	0.91	0.04%
145534	Anal atresia	Duplication	933288	GMDS-AS1	20466091	0.84	0.23%
59058	Arthrogryposis multiplex congenita	Duplication	840627	APOL4	21844811	0.84	0.25%
33260	Hearing impairment	Deletion	2641573	CLDN5	20466091	0.84	0.25%
59358	Attention deficit hyperactivity disorder	Deletion	2158318	INADL	21844811	0.83	0.29%
57809	Proteinuria	Deletion	4121281	AHSA1	21844811	0.83	0.29%
58696	Total anomalous pulmonary venous return	Duplication	6350820	KRT39	21844811	0.81	0.39%
155396	Tracheomalacia	Deletion	1865737	RGS14	20466091	0.80	0.54%
57591	Growth delay	Deletion	7912990	RFX4	21844811	0.79	0.58%
60244	Arachnoid cyst	Deletion	9625433	GTF2IRD2	21844811	0.78	0.65%
57341	Epispadias	Duplication	747247	MIR1243	21844811	0.77	0.80%
155202	Leukodystrophy	Deletion	1058291	GJA9-MYCBP	20466091	0.75	0.95%
153687	Sepsis	Deletion	5756016	DDX41	20466091	0.74	1.02%
57240	Ambiguous genitalia	Duplication	1500151	ATL2	21844811	0.72	1.16%
22234151	Polydactyly type 1	Duplication	926183	IHH	22234151	0.72	1.16%
25959774.1	F-syndrome Type 2	Inversion	1098179	WNT6	25959774	0.72	1.16%
18272352	Polydactyly	Deletion	623734	EPHA4	18272352	0.72	1.16%
57202	Pneumonia	Duplication	2914266	DGCR6	21844811	0.72	1.16%
33463	Microcephaly	Deletion	2734514	TXNRD2	20466091	0.72	1.16%
144137	Spina bifida occulta	Deletion	2785959	TTC3-AS1	20466091	0.70	1.43%

CR ID: ID in 3Disease Browser. Gene is the candidate gene name affected by CR events. SI Score (hESC) is calculated using hESC cell line’s data.