Table 2.

Genic and regulatory features significantly contribute to predicting transcriptional consequences of CNVs.

						CMC				CMC_HBCC
CNV class	Variable	Beta	SE	T	P	Beta	SE	T	P	Beta	SE	T	P
Deletions	Exonic Proportion	−1.7762	0.0664	−26.77	9.9E−158	−2.0563	0.0852	−24.12	1.8E−128	−1.5571	0.0939	−16.59	8.68E−62
	Enhancer sum	−0.0152	0.0083	−1.83	6.7E−02	−0.0093	0.0094	−0.99	3.2E−01	−0.0188	0.0112	−1.69	9.14E−02
	Promoter proportion	−0.1726	0.0589	−2.93	3.4E−03	−0.1719	0.0747	−2.30	2.1E−02	−0.0872	0.0843	−1.04	3.01E−01
	SV Length	−2.14E−07	1.46E-08	−14.70	6.9E−49	−1.92E−07	1.70E−08	−11.26	2.0E−29	−1.89E−07	3.42E−08	−5.53	3.19E−08
	Within TAD	−0.0090	0.0022	−4.03	5.7E−05	−0.0113	0.0031	−3.61	3.0E−04	−0.0046	0.0028	−1.65	9.83E−02
Duplications	Exonic Proportion	0.7825	0.0352	22.22	3.0E−109	1.1285	0.0546	20.67	1.0E−94	0.5043	0.0442	11.42	3.43E−30
	Enhancer sum	−0.0157	0.0027	−5.77	8.1E−09	0.0015	0.0062	0.24	8.1E−01	−0.0164	0.0030	−5.42	5.84E−08
	Promoter proportion	0.3735	0.0326	11.45	2.5E−30	0.3523	0.0509	6.92	4.5E−12	0.3438	0.0403	8.54	1.37E−17
	SV Length	3.99E-07	2.60E-08	15.34	4.6E−53	4.07E−07	3.52E−08	11.58	5.3E−31	3.05E−07	3.68E−08	8.30	1.04E−16
	Within TAD	0.0046	0.0036	1.26	2.1E−01	0.0072	0.0052	1.38	1.7E−01	0.0038	0.0045	0.86	3.89E−01

Coefficients of linear regression model to predict expression z-scores in deletions and duplications, across all samples and stratified by cohort.