The genomic coverage of three rare copy number variant regions that show strong association with endometriosis are depicted here.

The deletion at SGCZ on 8p22 (P = 7.3×10−4, OR = 8.5, Cl = 2.3–31.7) is shown in panel A, a deletion in MALRD1 on 10p12.31 (P = 5.6×10−4, OR = 14.1, Cl = 2.7–90.9) is shown in panel B, and a deletion at 11q14.1 (P = 5.7×10−4, OR = 33.8, Cl = 3.3–1651) is shown in panel C. The genomic coverage of CNVs observed in endometriosis cases are represented in red bars and the population controls in brown bars, with genes represented in blue. The red box on each ideogram shows the chromosomal location of the CNVs. To ensure correct CNV-calls in the three regions we performed a visual inspection of the LRR and BAF plots for all samples in the study population. LRR and BAF plots for each of the individuals represented above are shown in Figure S1 in File S2. CNVs with apparently identical boundaries were grouped as indicated by the number in parenthesis. Haplotypes in each group were compared to determine if the CNVs in each group have shared ancestral origin.