CNV/Phenotype associations significant at FDR=0.1
| CNV | Phenotype | No of controls (no of CNV carriers) | No of cases (no of CNV carriers) | Expected no of CNVs in cases | P-values | P-values B-H FDR | OR (95% CI) | Known finding |
| TAR dup | Obesity | 372 000 (385) | 9860 (23) | 10.2 | 0.00054 | 0.047 | 2.3 (1.5 to 3.4) | |
| 1q21.1 del | Heart failure | 376 477 (100) | 5081 (6) | 1.3 | 0.0011 | 0.083 | 5.3 (2.1 to 11.2) | Yes |
| 1q21.1 del | Cataract | 359 694 (92) | 21 864 (14) | 5.6 | 0.00047 | 0.042 | 3.2 (1.7 to 5.6) | Yes |
| 1q21.1 dup | Diabetes, type 2 | 360 864 (146) | 20 756 (22) | 8.4 | 0.00017 | 0.025 | 2.7 (1.6 to 4.1) | |
| NRXN1 del | Aneurysm | 379 638 (152) | 1971 (5) | 0.8 | 0.00042 | 0.041 | 7.6 (2.8 to 16.4) | |
| 2q13 dup | Diabetes, type 2 | 360 778 (60) | 20 745 (11) | 3.5 | 0.0012 | 0.094 | 3.4 (1.7 to 6.3) | |
| 3q29 dup | Any cancer | 331 757 (1) | 49 700 (4) | 0.15 | 6.23×10−5 | 0.011 | 37.5 (6.5 to 389.1) | |
| 3q29 dup | Diverticular disease intestine | 354 321 (2) | 27 136 (3) | 0.2 | 0.0001 | 0.017 | 41.8 (7.4 to 276.0) | |
| 3q29 dup | Inflammatory bowel disease | 362 864 (2) | 18 593 (3) | 0.1 | 0.00013 | 0.021 | 35.5 (6.7 to 217.8) | |
| 3q29 dup | Renal failure | 373 535 (3) | 7922 (2) | 0.1 | 0.00022 | 0.027 | 58.4 (9.2 to 324.8) | |
| 3q29 dup | Death | 370 486 (3) | 10 971 (2) | 0.1 | 0.0013 | 0.093 | 27.8 (4.5 to 146.0) | |
| 15q11q13 del BP3-BP4 | Gastric reflux | 347 165 (8) | 34 301 (6) | 0.8 | 0.00018 | 0.025 | 9.1 (3.1 to 25.4) | |
| 15q13.3 del | Diabetes, type 2 | 360 746 (28) | 20 743 (9) | 1.6 | 0.00038 | 0.039 | 4.9 (2.2 to 10.2) | |
| 15q13.3 del | Asthma | 332 151 (23) | 49 338 (14) | 3.4 | 0.00018 | 0.026 | 3.9 (2.0 to 7.4) | |
| 16p13.11 del | Obesity | 371 729 (114) | 9847 (10) | 3.0 | 0.0013 | 0.096 | 3.4 (1.7 to 6.2) | |
| 16p13.11 dup | Hypertension | 261 304 (483) | 120 931 (300) | 223.5 | 2.05×10−5 | 0.0043 | 1.4 (1.2 to 1.6) | |
| 16p13.11 dup | Death | 371 226 (743) | 11 009 (40) | 22.0 | 0.00097 | 0.080 | 1.8 (1.3 to 2.4) | |
| 16p12.1 del | Obesity | 371 827 (212) | 9860 (23) | 5.6 | 1.11×10−7 | 4.95×10-5 | 4.0 (2.5 to 6.0) | |
| 16p12.1 del | Hypertension | 260 945 (124) | 120 742 (111) | 57.4 | 8.64×10−8 | 5.41×10-5 | 2.1 (1.6 to 2.8) | |
| 16p12.1 del | Renal failure | 373 750 (218) | 7937 (17) | 4.6 | 7.23×10−6 | 0.0021 | 3.8 (2.3 to 6.1) | |
| 16p12.1 del | Diabetes, type 2 | 360 926 (208) | 20 761 (27) | 12.0 | 0.00021 | 0.028 | 2.3 (1.5 to 3.5) | |
| 16p12.1 del | Heart other | 369 848 (217) | 11 839 (18) | 6.9 | 0.00029 | 0.034 | 2.8 (1.7 to 4.4) | Yes |
| 16p12.1 del | Ureter/bladder | 333 111 (186) | 48 576 (49) | 27.1 | 0.00033 | 0.036 | 1.9 (1.3 to 2.5) | |
| 16p12.1 del | Respiratory | 360 911 (209) | 20 776 (26) | 12.0 | 0.00069 | 0.059 | 2.2 (1.4 to 3.2) | |
| 16p11.2 distal del | Gout | 374 410 (48) | 7096 (6) | 0.9 | 0.00046 | 0.042 | 6.5 (2.5 to 14.4) | |
| 16p11.2 distal del | Obesity | 371 660 (45) | 9846 (9) | 1.2 | 1.14×10−5 | 0.0028 | 7.1 (3.3 to 13.7) | Yes |
| 16p11.2 distal del | Diabetes, type 2 | 360 757 (39) | 20 749 (15) | 2.2 | 8.86×10−8 | 4.63×10−5 | 7.0 (3.7 to 12.6) | |
| 16p11.2 del | Diabetes, type 2 | 360 794 (76) | 20 761 (27) | 4.4 | 2.54×10−11 | 3.98×10−8 | 6.1 (3.8 to 9.5) | Secondary |
| 16p11.2 del | Obesity | 371 699 (84) | 9856 (19) | 2.2 | 7.39×10−10 | 7.71×10−7 | 6.8 (4.0 to 11.0) | Yes |
| 16p11.2 del | Anaemia | 362 396 (84) | 19 159 (19) | 4.4 | 2.15×10−6 | 0.00075 | 4.0 (2.4 to 6.5) | |
| 16p11.2 del | Asthma | 332 199 (71) | 49 356 (32) | 10.5 | 1.33×10−5 | 0.0030 | 2.7 (1.8 to 4.1) | |
| 16p11.2 del | Renal failure | 373 625 (93) | 7930 (10) | 2.0 | 6.04×10−5 | 0.012 | 5.1 (2.5 to 9.5) | |
| 16p11.2 del | Hypertension | 260 873 (52) | 120 682 (51) | 24.1 | 9.44×10−6 | 0.0025 | 2.6 (1.7 to 3.8) | Secondary |
| 16p11.2 del | Osteoarthritis | 312 820 (73) | 68 735 (30) | 16.0 | 0.00031 | 0.035 | 2.4 (1.5 to 3.6) | Secondary |
| 16p11.2 dup | Irritable bowel syndrome | 368 567 (118) | 13 016 (13) | 4.2 | 0.00036 | 0.037 | 3.3 (1.8 to 5.7) | |
| 16p11.2 dup | Sciatica | 338 444 (103) | 43 139 (28) | 13.1 | 0.001 | 0.083 | 2.1 (1.4 to 3.2) | |
| 17p12 HNPP del | Neuropathies | 365 743 (194) | 15 928 (25) | 8.4 | 5.44×10−6 | 0.0017 | 3.0 (2.0 to 4.5) | Yes |
| 17p12 CMT1A dup | Neuropathies | 365 609 (60) | 15 959 (56) | 2.6 | 3.9×10−124 | 1.2×10−120 | 21.8 (15.0 to 31.5) | Yes |
| 17p12 CMT1A dup | Anaemia | 362 411 (99) | 19 157 (17) | 5.2 | 6.7×10−5 | 0.012 | 3.3 (1.9 to 5.4) | |
| 17p12 CMT1A dup | Stroke | 372 741 (107) | 8827 (9) | 2.5 | 0.0013 | 0.094 | 3.7 (1.8 to 6.9) | |
| 17q12 del | Diabetes insulin dependent | 378 861 (3) | 2598 (4) | 0.0 | 3.93×10−8 | 3.08×10−5 | 135.9 (31.2 to 641.1) | Yes |
| 17q12 del | Digestive | 299 609 (1) | 81 850 (6) | 0.3 | 0.00044 | 0.042 | 15.4 (3.2 to 150.3) | |
| 17q12 dup | Renal failure | 373 622 (90) | 7929 (9) | 1.9 | 0.00029 | 0.035 | 4.6 (2.2 to 8.6) | |
| 22q11.2 dup | Hernia | 333 779 (215) | 47 939 (51) | 30.9 | 0.0013 | 0.094 | 1.7 (1.2 to 2.3) | |
| 22q11.2 dup | Gastric reflux | 347 374 (217) | 34 344 (49) | 21.5 | 1.82×10−6 | 0.0007 | 2.3 (1.7 to 3.1) | |
| 22q11.2 distal del | Aneurysm | 379 490 (4) | 1967 (1) | 0.0 | 0.0013 | 0.092 | 104.9 (9.7 to 673.6) |
The numbers of cases and controls are the numbers of people who have the phenotype. The ‘Expected number of CNVs in cases’ is extrapolated from their frequencies in the controls. Uncorrected p-values and Benjamini-Hochberg FDR corrected p-values for 3132 tests (p-value B-H FDR) are also shown. OR and 95% CI of the OR are produced by Firth’s logistic regression analysis (Methods section). More details are given in online supplementary tables 6 and 7. ‘Known finding’ refers to known medical consequences, listed in online supplementary table 1, or to phenotypes that appear a consequence of the known ones (marked as ‘secondary’ in the table, as discussed below).
FDR, false discovery rate.