Table 2. Top regions of genetic association for each meta-analysis.
| Chr | Index SNP | A1/A2 | Freq | OR | P-value | N | Position | KB | Genes |
|---|---|---|---|---|---|---|---|---|---|
| Responders vs non-responders, subjective assessments | |||||||||
| 20 | rs73918339 | T/C | 0.91 | 0.56 | 3.80 × 10−7 | 60 | 61150190–61213367 | 63 | MIR133A2, MIR1-1, C20orf200, C20orf166 |
| 18 | rs7240206 | C/G | 0.09 | 0.60 | 3.86 × 10−7 | 67 | 74393681–74447380 | 54 | LOC105372213 |
| 7 | rs116927879 | G/A | 0.85 | 1.53 | 4.99 × 10−7 | 267 | 45588502–46011988 | 423 | SEPT7P2, IGFBP3, IGFBP1, ADCY1 |
| 4 | rs78295376 | T/C | 0.90 | 0.57 | 6.77 × 10−7 | 26 | 76480371–76729937 | 250 | USO1, TMSL3, G3BP2, FRG2, CDKL2, C4orf26 |
| Responders vs non-responders, objective assessments | |||||||||
| 6 | rs438475 | G/A | 0.88 | 0.49 | 2.13 × 10−6 | 165 | 31 770265–32625494 | 855 | NOTCH4, many genes in MHC region |
| 11 | rs113262272 | A/− | 0.71 | 1.93 | 3.77 × 10−6 | 99 | 99298992–99587113 | 288 | CNTN5 |
| 14 | rs809 | C/T | 0.53 | 0.61 | 4.08 × 10−6 | 39 | 78502019–78558331 | 56 | NRXN3 |
| 6 | rs181812561 | G/A | 0.98 | 0.13 | 6.39 × 10−6 | 3 | 75079066–75231552 | 152 | LOC101928516 |
| Responders vs controls, subjective assessments | |||||||||
| 1 | rs12144699 | G/A | 0.96 | 0.60 | 6.05 × 10−7 | 7 | 59605197–59863936 | 259 | OR4F16, OR4F29, LOC729467, LOC100133331, LOC100132287, FGGY |
| 3 | rs9834970 | T/C | 0.50 | 0.82 | 7.88 × 10−7 | 153 | 36834099–37285522 | 451 | TRANK1, MLH1, MIR4273, LRRFIP2, GOLGA4, FRG2C, EPM2AIP1 |
| 3 | rs12493050 | G/A | 0.20 | 1.27 | 8.78 × 10−7 | 276 | 182478533–182909924 | 431 | MCF2L2, MCCC1, LAMP3, DCUN1D1, ATP11B |
| 7 | rs4947962 | G/C | 0.11 | 1.35 | 1.35 × 10−6 | 85 | 54906722–55161372 | 255 | EGFR |
| Responders vs controls, objective assessments | |||||||||
| 11 | rs146727601 | −/TA | 0.01 | 3.98 | 1.33 × 10−8 | 2 | 112118590–112343856 | 225 | PTS, PLET1 |
| 2 | rs116323614 | A/G | 0.03 | 3.14 | 2.74 × 10−8 | 58 | 179859406–180139219 | 280 | SESTD1, CCDC141 |
| 19 | rs77866734 | C/T | 0.98 | 0.27 | 1.49 × 10−7 | 11 | 1633923–1642221 | 8 | TCF3, KIR3DP1, KIR2DL4 |
| 17 | rs142643109 | T/G | 0.98 | 0.28 | 3.93 × 10−7 | 3 | 60086587–60497572 | 411 | TBC1D3P2, MIR4315-2, MIR4315-1, METTL2A, MED13, EFCAB3 |
Abbreviations: A1/A2, reference and alternate allele; Chr, chromosome; Freq, frequency of reference allele; Index SNP, the single-nucleotide polymorphism with the strongest association in the genomic region; MHC, major histocompatibility complex; N, number of SNPs in the reported region; OR, odds ratio. We used LD clumping to define regions of association. Positions are given in UCSC hg19 coordinates. Lines in bold indicate associations that are genome-wide statistically significant.