Table 3.
All distinct loci associated with GGE at conjFDR < 0.05
| CHR | LEAD_SNP | Nearest gene | A1/A2 | P-value | Novel in epilepsy | Psychiatric disorder shared with | Concord effect |
|---|---|---|---|---|---|---|---|
| 2 | rs6708889 | MRPL33:RBKS | T/C | 6.22 × 10−5 | Novel | BIP, SCZ | Yes |
| 2 | rs1040225 | VRK2 | G/A | 1.53 × 10−10 | ILAE 2014 | SCZ, DEP | No |
| 2 | rs6715448 | RN7SL201P | C/T | 8.24 × 10−5 | Novel | BIP | No |
| 2 | rs1673468 | AC018880.2 | T/C | 4.30 × 10−5 | ILAE25 | ASD | No |
| 2 | rs249697 | AC009227.3 | A/G | 7.90 × 10−5 | Novel | SCZ | No |
| 2 | rs6714133 | SATB2:SATB2-AS1 | G/T | 1.60 × 10−4 | Novel | SCZ | Yes |
| 3 | rs17194427 | CNTN4 | C/A | 1.25 × 10−4 | Novel | SCZ | Yes |
| 3 | rs10428260 | TBC1D5 | A/G | 1.85 × 10−5 | Novel | SCZ | Yes |
| 3 | rs75298156 | RP11-944L7.4:ZNF197 | A/G | 2.14 × 10−4 | Novel | SCZ | Yes |
| 3 | rs62256903 | SMIM4 | G/A | 2.30 × 10−4 | Novel | SCZ | No |
| 3 | rs3804640 | CD47 | A/G | 1.20 × 10−5 | Novel | BIP, SCZ | Yes |
| 3 | rs4678442 | RP11-731C17.1 | A/G | 5.06 × 10−5 | Novel | SCZ | No |
| 4 | rs6448744 | PCDH7 | T/G | 4.20 × 10−8 | ILAE 2014 | ADHD, SCZ | No |
| 5 | rs434517 | RP11-492A10.1 | C/A | 7.25 × 10−7 | ILAE2 | ASD | No |
| 5 | rs4515335 | PPP2R2B | G/A | 1.27 × 10−4 | Novel | SCZ | No |
| 5 | rs815624 | MFAP3 | T/C | 2.10 × 10−4 | Novel | SCZ | No |
| 6 | rs2260000 | PRRC2A | C/T | 2.40 × 10−5 | Novel | SCZ, DEP | Yes |
| 6 | rs1572208 | RIMS1 | T/C | 1.03 × 10−5 | Novel | SCZ | Yes |
| 6 | rs7742212 | PTPRK | A/G | 9.10 × 10−6 | ILAE2 | SCZ | Yes |
| 7 | rs12704290 | GRM3 | G/A | 5.03 × 10−6 | Song et al.52 | SCZ | No |
| 8 | rs7016267 | FAM49B | C/T | 2.60 × 10−4 | Novel | SCZ | Yes |
| 8 | rs11782665 | AC138647.1 | A/C | 8.40 × 10−5 | Novel | ASD | Yes |
| 9 | rs13290882 | KIF27 | G/A | 1.16 × 10−5 | ILAE25 | ADHD | Yes |
| 10 | rs1873691 | KCNMA1 | G/A | 1.19 × 10−4 | Novel | SCZ | No |
| 11 | rs174605 | FADS2 | G/T | 2.87 × 10−5 | Novel | BIP | No |
| 11 | rs56186611 | HNRNPA1P60 | C/T | 1.53 × 10−4 | Novel | SCZ | No |
| 13 | rs73550679 | HS6ST3 | C/T | 4.17 × 10−5 | Novel | SCZ | No |
| 14 | rs12885033 | MDGA2:MDGA2 | A/C | 7.20 × 10−5 | Novel | BIP | Yes |
| 14 | rs55643369 | CTD-2315A10.2 | T/C | 7.56 × 10−5 | Novel | SCZ | Yes |
| 15 | rs2055891 | HOMER2 | A/G | 3.10 × 10−5 | Novel | BIP, SCZ | No |
| 16 | rs4350587 | RBFOX1 | A/G | 1.40 × 10−4 | ILAE25 | SCZ | Yes |
| 16 | rs12325539 | DOC2A | T/C | 4.00 × 10−5 | Novel | SCZ | No |
| 16 | rs72790284 | CNOT1 | C/T | 2.11 × 10−4 | Novel | SCZ | Yes |
| 16 | rs13333786 | AC010547.9:ZNF19 | T/C | 9.40 × 10−5 | Novel | SCZ | Yes |
| 17 | rs8071147 | PRPSAP2 | G/A | 1.44 × 10−4 | Novel | SCZ | Yes |
| 17 | rs2306593 | MYO19 | T/C | 3.00 × 10−4 | Novel | SCZ | Yes |
| 17 | rs4473241 | CTB-175E5.7 | G/T | 8.40 × 10−6 | Novel | BIP | No |
| 20 | rs3829704 | ZNF512B:LINC00176 | C/T | 8.70 × 10−5 | Novel | BIP | No |
| 22 | rs133568 | MIR3201 | A/G | 2.50 × 10−6 | Novel | SCZ | No |
P-values are reported for the epilepsy phenotype. Detailed information about the reported loci can be found in Supplementary Tables 1–8. BIP = bipolar disorder; DEP = depression; SCZ = schizophrenia.