Table 2. Index SNPs for strongest associations for responders or non-responders vs healthy controls, and non-TRD or TRD vs healthy controls.
| Cytoband | SNP | CHR | BP | Alleles | P-value | OR | 95% CI | Gene context |
|---|---|---|---|---|---|---|---|---|
| NDRI non-responder vs healthy controls | ||||||||
| Xq27.2 | rs190783615 | X | 141860406 | C/T | 2.0 × 10−7 | 15.18 | 3.095, 74.439 | MAGEC2—-[]—-SPANXN4 |
| 5p13.1 | rs201203751 | 5 | 39203597 | D/I | 5.0 × 10−7 | 4.009 | 2.537, 6.336 | [FYB] |
| 17q11.2 | rs183124483 | 17 | 26437054 | A/G | 5.9 × 10−7 | 0.067 | 0.031, 0.146 | [NLK] |
| 5p12 | rs56388524 | 5 | 45757561 | C/T | 6.8 × 10−7 | 1.798 | 1.451, 2.228 | HCN1—[] |
| 5q12.3 | rs143405544 | 5 | 64755604 | A/G | 7.0 × 10−7 | 0.149 | 0.054, 0.410 | [ADAMTS6] |
| 20q12 | rs183042538 | 20 | 39826060 | A/T | 7.7 × 10−7 | 1.431 | 1.249, 1.638 | [ZHX3] |
| NDRI responders vs healthy controls | ||||||||
| 12p12.1 | rs200855945 | 12 | 26277893 | D/I | 4.4 × 10−7 | 4.929 | 2.350, 10.340 | [BHLHE41] |
| 4q35.1 | rs112538845 | 4 | 185005628 | C/T | 5.6 × 10−7 | 1.637 | 1.366, 1.961 | STOX2—[]-ENPP6 |
| 2q36.2 | rs78087832 | 2 | 225464777 | C/T | 5.7 × 10−7 | 2.731 | 1.933, 3.857 | CUL3—[]—-DOCK10 |
| 9q33.1 | rs112106319 | 9 | 117856818 | A/T | 1.1 × 10−6 | 0.43 | 0.294, 0.627 | [TNC] |
| 12q21.2 | rs73425402 | 12 | 77897298 | A/T | 1.4 × 10−6 | 0.048 | 0.019, 0.121 | E2F7—-[]—-NAV3 |
| SSRI non-responders vs healthy controls | ||||||||
| 11p15.3 | rs1994321 | 11 | 12087313 | G/T | 5.2 × 10−7 | 0.866 | 0.818, 0.916 | DKK3—[]—MICAL2 |
| 2p25.1 | rs113378111 | 2 | 9928153 | A/G | 6.9 × 10−7 | 1.579 | 1.303, 1.912 | YWHAQ—-[]—TAF1B |
| 5q31.1 | rs73788091 | 5 | 132765209 | C/T | 1.2 × 10−6 | 3.011 | 2.044, 4.437 | [FSTL4] |
| 18q22.1 | rs9951011 | 18 | 65033678 | A/G | 1.8 × 10−6 | 0.847 | 0.792, 0.906 | CDH19—-[]—-DSEL |
| 1q31.1 | rs78620960 | 1 | 190781499 | A/G | 2.0 × 10−6 | 0.831 | 0.771, 0.896 | FAM5C—-[] |
| SSRI responders vs healthy controls | ||||||||
| 4q31.23 | rs150175932 | 4 | 151022647 | C/T | 1.0 × 10−7 | 15.22 | 3.318, 69.804 | [DCLK2] |
| 8q12.1 | rs141746753 | 8 | 57846713 | C/T | 1.2 × 10−6 | 0.308 | 0.175, 0.544 | PENK—-[]—IMPAD1 |
| 7q31.33 | rs73720034 | 7 | 125435049 | C/T | 1.3 × 10−6 | 1.256 | 1.142, 1.381 | POT1—-[]—-GRM8 |
| 2p16.1 | rs6545694 | 2 | 58847953 | A/G | 1.7 × 10−6 | 1.096 | 1.056, 1.137 | FANCL—-[] |
| 2p25.3 | rs61519662 | 2 | 2700391 | C/T | 2.4 × 10−6 | 0.908 | 0.872, 0.945 | MYT1L—-[]—-TSSC1 |
| Citalopram or escitalopram non-responders vs healthy controls | ||||||||
| 20q13.13 | rs6063349 | 20 | 47681882 | C/G | 6.9 × 10−7 | 0.845 | 0.790, 0.903 | [CSE1L] |
| 11p13 | rs142641502 | 11 | 33131407 | C/T | 8.4 × 10−7 | 4.565 | 2.155, 9.671 | [CSTF3] |
| 6p25.3 | rs201569130 | 6 | 1403150 | D/I | 8.6 × 10−7 | 3.009 | 1.785, 5.073 | FOXF2-[]—-FOXC1 |
| 15q23 | rs1548076 | 15 | 70226623 | A/G | 1.2 × 10−6 | 0.401 | 0.262, 0.615 | RPLP1—-[]—-TLE3 |
| 11q13.2 | rs182377406 | 11 | 67216849 | A/G | 1.3 × 10−6 | 5.773 | 3.250, 10.254 | CORO1B-[]-GPR152 |
| Citalopram or escitalopram responders vs healthy controls | ||||||||
| 11q14.1 | rs74860738 | 11 | 80382727 | A/G | 3.2 × 10−7 | 0.777 | 0.708, 0.854 | [] |
| 20p11.23 | rs143934587 | 20 | 19146450 | A/G | 6.5 × 10−7 | 0.149 | 0.080, 0.277 | C20orf78—-[]—SLC24A3 |
| 4q12 | rs189864513 | 4 | 53633557 | C/T | 7.8 × 10−7 | 0.081 | 0.037, 0.177 | ERVMER34-1—[]—RASL11B |
| 3q27.3 | rs11924809 | 3 | 186071445 | A/G | 1.3 × 10−6 | 1.215 | 1.122, 1.316 | [DGKG] |
| 10q24.33 | rs117375960 | 10 | 104921664 | A/C | 1.5 × 10−6 | 0.007 | 0.000, 0.345 | [NT5C2] |
| TRD vs healthy controls | ||||||||
| 21q22.2 | rs190544851 | 21 | 39732396 | G/T | 2.8 × 10−7 | 14.29 | 3.555, 57.454 | KCNJ15—[]—ERG |
| 6q25.3 | rs57043326 | 6 | 159314933 | A/G | 8.2 × 10−7 | 0.377 | 0.240, 0.593 | [C6orf99] |
| 1p36.21 | rs12068879 | 1 | 15286356 | A/G | 1.1 × 10−6 | 2.221 | 1.667, 2.958 | [KAZN] |
| 9p23 | rs1322281 | 9 | 10582445 | C/T | 1.4 × 10−6 | 1.242 | 1.139, 1.354 | [PTPRD] |
| 2p22.3 | rs13418410 | 2 | 33800899 | A/C | 1.6 × 10−6 | 1.212 | 1.121, 1.311 | RASGRP3—[]-FAM98A |
| Non-TRD vs healthy controls | ||||||||
| 12q13.13 | rs34807503 | 12 | 51919133 | D/I | 4.5 × 10−7 | 0.917 | 0.887, 0.948 | SLC4A8-[]—SCN8A |
| 7q32.2 | rs2402960 | 7 | 129405774 | C/T | 7.5 × 10−7 | 0.91 | 0.877, 0.945 | NRF1-[]—UBE2H |
| 16q21 | rs200312707 | 16 | 62065679 | D/I | 1.4 × 10−6 | 0.919 | 0.888, 0.951 | [CDH8] |
| 1p36.23 | rs400736 | 1 | 8078309 | C/T | 1.9 × 10−6 | 0.921 | 0.891, 0.953 | [ERRFI1] |
| 1p32.3 | rs35265457 | 1 | 54273279 | C/T | 2.0 × 10−6 | 1.508 | 1.261, 1.803 | [NDC1] |
Abbreviations: BP, base pairs; CI, confidence interval; NDRI, norepinephrine–dopamine reuptake inhibitor; OR, odds ratio; SNP, single-nucleotide polymorphism; SSRI, selective serotonin reuptake inhibitor; TRD, treatment-resistant depression.
The table of index SNPs shows information for the most-associated SNP in each associated region, for at least 5 and at most 50 regions for each phenotype. Regions are defined by identifying SNPs with P<10−5, then grouped into intervals separated by gaps of at least 250 kb. The SNP with smallest P within each interval was chosen as index SNP for the region.