Table 2.

Homozygous deletion CNVRs associated with a major disease category.

Pheno	Chr:Pos (hg18)	P-value	Cases	Controls	Gene name	Phenotype information
Cardio	chr11:55204003–55204003	8.0E–10	157	1204	OR4C6	Obesity [21131291]
Cancer	chr11:81194909–81194909	2.9E–07	80	129	BC041900	Target of FOXF2; deficiency important in E > M transition
Neuro	chr1:78432711–78432711	6.1E–06	20	6	AX747165, BC015860	Missense (c.785C > T; p.L262R) and nonsense (c.903G > A; p.W301X) mutations in human GIPC3 cause congenital sensorineural hearing impairment
Aid	chr1:167466049–167466049	3.0E–05	15	6	NME7	Venous thromboembolism
Neuro	chr13:97328242–97330758	3.8E–05	28	16	IPO5	Schizophrenia
Neuro	chr6:67105019–67105019	4.1E–05	97	110	EYS	AR retinitis pigmentosa
Cardio	chr5:113188389–113197319	4.2E–05	34	195	YTHDC2	mRNA metabolism
Aid	chr3:191217916–191217916	4.5E–05	28	23	LEPREL1	Homozygous loss-of-function mutation causes severe non-syndromic high myopia with early-onset cataracts.
Aid	chr12:27539678–27545813	8.1E–05	10	2	PPFIBP1	Receptor tyrosine kinase
Neuro	chr3:163625169–163625169	1.1E–04	57	55	BC073807	NA
Aid	chr5:117421055–117421055	2.5E–04	79	124	BC044609	NA
Neuro	chr19:40354649–40354649	2.6E–04	51	49	FXYD5	NA
Neuro	chr15:50050557–50057972	2.7E–04	12	3	LEO1	Neural tube development [20178782]
Aid	chr3:75511365–75532825	3.8E–04	57	82	DQ584669	N/A

CNVRs presented in Table 2 are select loci from those that reached experimentally defined statistical significance (P < 5 × 10⁻⁴), which adjusts for multiple comparisons based on results obtained from repeated simulations (see Methods). See Supplementary Data 6 for additional loci that are marginally associated with at least one disease category