Table 3. Most significant interactions (overall and among those that were nominally replicated), by condition; FastEpistasis with logistic regression.
| Condition/Rank | SNP1 | SNP2 | Discovery | Replication | Rep.? | Anno1 | Anno2 | Gene1 | Gene2 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RSID | Chr | A1 | A0 | RSID | Chr | A1 | A0 | FE, P | Unadj., P | Adj., OR | Adj., P | Unadj., P | Adj., OR | Adj., P | ||||||
| Allergic rhinitis | ||||||||||||||||||||
| 1 | rs493725 | 11 | C | T | rs12456095 | 18 | A | G | 1.49E-10 | 1.52E-10 | 1.21 (1.14, 1.28) | 8.61E-11 | 6.10E-01 | 0.94 (0.78, 1.13) | 5.29E-01 | No | G | KIRREL3 | ||
| 74 | rs10710098 | 12 | – | A | rs837473 | 12 | G | A | 1.69E-09 | 2.33E-09 | 1.22 (1.14, 1.30) | 2.08E-09 | 2.39E-02 | 1.27 (1.03, 1.57) | 2.48E-02 | Yes | G | PPFIBP1 | ||
| Asthma | ||||||||||||||||||||
| 1 | rs6764801 | 3 | G | T | rs4574345 | 4 | C | T | 2.57E-11 | 2.84E-11 | 1.27 (1.19, 1.37) | 2.50E-11 | 1.11E-01 | 1.20 (0.98, 1.47) | 7.62E-02 | No | ||||
| 19 | rs7480608 | 11 | A | C | rs996197 | 20 | A | C | 8.41E-10 | 8.31E-10 | 0.79 (0.73, 0.85) | 3.53E-10 | 5.40E-02 | 0.81 (0.65, 1.00) | 4.68E-02 | Yes | G | C20orf26 | ||
| Cardiac disease | ||||||||||||||||||||
| 1 | rs1407721 | 1 | T | G | rs455326 | 5 | A | G | 5.09E-10 | 6.86E-10 | 1.22 (1.15, 1.29) | 1.64E-11 | 4.28E-01 | 1.01 (0.84, 1.22) | 8.97E-01 | No | ||||
| 100 | rs9322768 | 6 | C | T | rs6463841 | 7 | G | A | 7.47E-09 | 6.54E-09 | 0.86 (0.82, 0.91) | 4.19E-09 | 6.08E-02 | 0.80 (0.69, 0.94) | 7.20E-03 | Yes | G | NXPH1 | ||
| Depression | ||||||||||||||||||||
| 1 | rs16912862 | 9 | G | A | rs4769180 | 13 | C | T | 7.78E-11 | 5.40E-11 | 0.79 (0.74, 0.85) | 1.81E-11 | 9.92E-01 | 1.00 (0.85, 1.17) | 9.56E-01 | No | G | ZNF169 | ||
| 3 | rs7587468 | 2 | G | A | rs13120959 | 4 | T | G | 1.16E-10 | 6.72E-11 | 0.80 (0.75, 0.86) | 1.26E-10 | 5.17E-02 | 0.84 (0.71, 0.99) | 3.51E-02 | Yes | G | PRSS12 | ||
| Dermatophytosis | ||||||||||||||||||||
| 1 | rs4456135 | 1 | C | T | rs12162346 | 2 | T | C | 1.76E-12 | 2.02E-12 | 1.29 (1.20, 1.38) | 4.29E-13 | 1.43E-01 | 0.87 (0.74, 1.04) | 1.23E-01 | No | G | LPHN2 | ||
| 17 | rs4318363 | 2 | C | T | rs7896441 | 10 | G | A | 3.02E-10 | 4.45E-10 | 1.23 (1.16, 1.32) | 1.98E-10 | 3.54E-02 | 1.19 (1.01, 1.39) | 3.27E-02 | Yes | G | TACC2 | ||
| Diabetes, type 2 | ||||||||||||||||||||
| 1 | rs6677074 | 1 | A | C | rs34332506 | 3 | C | T | 4.84E-10 | 5.33E-10 | 0.79 (0.73, 0.85) | 1.02E-10 | 8.66E-01 | 1.00 (0.84, 1.18) | 9.81E-01 | No | G | G | CASQ2 | PCOLCE2 |
| 8 | rs4986223 | 18 | C | T | rs59493447 | 22 | T | G | 3.29E-10 | 8.47E-10 | 1.33 (1.22, 1.45) | 3.11E-10 | 2.83E-02 | 1.26 (1.01, 1.57) | 3.65E-02 | Yes | G | D, G | BC040860 | SREBF2 |
| Dyslipidemia | ||||||||||||||||||||
| 1 | rs3860935 | 9 | T | C | rs12243792 | 10 | A | G | 8.90E-11 | 8.99E-11 | 1.20 (1.14, 1.26) | 1.09E-11 | 7.29E-01 | 1.03 (0.86, 1.24) | 7.56E-01 | No | G | G, M | FRMD3 | ZNF248 |
| 57 | rs1655483 | 11 | G | A | rs2617815 | 19 | G | A | 4.51E-09 | 4.18E-09 | 1.18 (1.12, 1.25) | 1.69E-09 | 3.22E-03 | 1.28 (1.05, 1.56) | 1.33E-02 | Yes | R, G | VAV1 | ||
| Hemorrhoids | ||||||||||||||||||||
| 1 | rs12043442 | 1 | C | T | rs16858754 | 3 | T | C | 4.92E-11 | 2.00E-11 | 0.71 (0.65, 0.79) | 1.05E-11 | 3.08E-01 | 0.88 (0.69, 1.13) | 3.21E-01 | No | ||||
| 7 | rs2564056 | 2 | C | T | rs13421607 | 2 | T | C | 1.14E-10 | 1.99E-10 | 1.22 (1.15, 1.30) | 2.44E-10 | 1.31E-02 | 1.25 (1.06, 1.48) | 8.07E-03 | Yes | ||||
| Hypertensive disease | ||||||||||||||||||||
| 1 | rs10187912 | 2 | A | G | rs9929738 | 16 | G | A | 9.09E-10 | 9.27E-10 | 0.82 (0.77, 0.87) | 1.41E-11 | 1.91E-01 | 0.92 (0.74, 1.15) | 4.63E-01 | No | ||||
| 87 | rs7519626 | 1 | C | T | rs17342461 | 4 | C | T | 1.52E-08 | 1.39E-08 | 0.87 (0.83, 0.91) | 2.20E-09 | 9.65E-02 | 0.84 (0.71, 0.99) | 4.12E-02 | Yes | ||||
| Osteoarthritis | ||||||||||||||||||||
| 1 | rs7316595 | 12 | C | T | rs2066936 | 19 | G | A | 1.05E-09 | 1.05E-09 | 0.85 (0.81, 0.89) | 1.86E-11 | 9.77E-01 | 1.06 (0.90, 1.24) | 5.03E-01 | No | G | G | LOC643339 | ZNF773 |
| 6 | rs272051 | 2 | G | A | rs7630522 | 3 | T | C | 1.08E-08 | 1.01E-08 | 1.18 (1.13, 1.25) | 1.33E-10 | 5.87E-02 | 1.22 (1.01, 1.46) | 3.42E-02 | Yes | ||||
Interactions were first analyzed with FastEpistasis and then subjected to a follow-up analysis with logistic regression. For each condition, the most significant of all interactions is listed, followed by the most significant interaction that was nominally replicated. Interactions were ranked by significance in the adjusted logistic regression analysis (discovery). Numbers in the leftmost column indicate the overall ranks of the interactions for the respective condition. Blanks in the “Anno” or “Gene” columns indicate no annotation or gene assigned to the respective SNP. SNP, single nucleotide polymorphism; Rep.?, whether or not the interaction was nominally replicated; Anno1/Anno2, annotation assigned to SNP1 or SNP2, respectively; Gene1/Gene2, gene assigned to SNP1 and SNP2, respectively; RSID, reference SNP cluster ID; Chr, chromosome number; A1, nonreferent allele; A0, referent allele. FE, P, P-value from the FastEpistasis analysis; Unadj., P, P-value from the unadjusted logistic regression analysis; Adj., OR, interaction odds ratio and 95% confidence interval, from the adjusted logistic regression analysis; Adj., P, P-value from the adjusted logistic regression analysis; All “adjusted” analyses were adjusted for the first two principal components, birth year category, and sex; G, any-gene; D, disease-gene; M, marginal; R, regulatory.