Table 1. Ras/MAPK ASD epistasis top results.
The unique epistatic SNP pairs with P < 2.9x10-9 are listed in the table. For each SNP, the following is listed in order of columns: rsID (Epistatic SNP), chromosome (CHR), position (BP, reference version hg19), minor allele frequency in the ASD dataset (MAF), nearest gene to the epistatic SNP, Ras/MAPK gene associated with the interacting SNP, and P-value for epistasis in cases (Epistasis ASD P) and pseudo-controls (Epistasis Control P). Locus pairs meeting genome-wide significance criteria (P < 7.6 x 10−10) are bolded. Main effects for epistatic and Ras/MAPK SNPs listed here are listed in S4 Table, with no SNPs showing P < 0.01.
| Epistatic SNP | CHR | BP | MAF | Nearest gene (epistatic SNP) | Ras/ MAPK pathway gene | Epistasis ASD P | Epistasis control P |
|---|---|---|---|---|---|---|---|
| rs149565205 | 3 | 6,539,899 | 0.03 | EDEM1 / GRM7 | PTPN11 | 7.3x10-11 | 0.018 |
| rs114490548 | 7 | 3,8139,570 | 0.02 | EPDR1 / STARD3NL | RASA1 | 7.8x10-11 | 0.39 |
| rs2441690 | 11 | 127,107,790 | 0.06 | KIRREL3 / ETS1 | MAPK1 | 1.0x10-10 | 0.17 |
| rs62168052 | 2 | 135,088,091 | 0.03 | MGAT5 | SPRED1 | 1.1x10-10 | 0.21 |
| rs304654 | 4 | 124,123,184 | 0.02 | SPATA5 | SOS1 | 1.1x10-10 | 0.93 |
| rs56667163 | 3 | 136,773,620 | 0.06 | IL20RB / SOX14 | RASA1 | 1.6x10-10 | 0.73 |
| chr15:71697182:D | 15 | 71,697,182 | 0.02 | THSD4 | RAF1 | 1.6x10-10 | 0.25 |
| rs78762238 | 13 | 64,302,181 | 0.03 | PCDH20/ PCDH9 | NF1 | 2.5x10-10 | 9.4x10-3 |
| rs41274082 | 10 | 65,381,281 | 0.02 | REEP3 | MAP2K1 | 2.6x10-10 | 0.70 |
| rs60709797 | 15 | 23,004,989 | 0.03 | NIPA2 | PTPN11 | 2.7x10-10 | 9.9x10-3 |
| rs11925140 | 3 | 112,842,425 | 0.02 | GTPBP8 / BOC | NF1 | 3.7x10-10 | 0.05 |
| rs57173428 | 1 | 55,100,883 | 0.02 | ACOT11 / TTC4 | KRAS | 3.8x10-10 | 0.25 |
| rs1826547 | 8 | 27,414,024 | 0.03 | EPHX2 / SCARA3 | BRAF | 4.0x10-10 | 0.48 |
| rs17110869 | 1 | 55,108,237 | 0.02 | MROH7 | KRAS | 4.5x10-10 | 0.26 |
| rs80179511 | 6 | 154,274,998 | 0.06 | RGS17 / OPRM1 | RAF1 | 5.3x10-10 | 0.16 |
| rs140695911 | 10 | 29,495,250 | 0.02 | BAMBI / LYZL1 | KRAS | 5.9x10-10 | 0.29 |
| rs28459694 | 1 | 158,355,190 | 0.03 | CD1E / OR10T2 | MAPK1 | 6.2x10-10 | 0.28 |
| rs73760016 | 5 | 19,469,048 | 0.03 | BASP1 / CDH18 | SPRED1 | 6.8x10-10 | 0.036 |
| rs192196641 | 10 | 8,587,332 | 0.04 | GATA3 / CELF2 | MAP2K1 | 6.8x10-10 | 0.062 |
| rs80214471 | 5 | 66,139,877 | 0.03 | MAST4 | MAP2K1 | 8.4x10-10 | 0.60 |
| rs2765709 | 10 | 25,507,753 | 0.10 | GPR158 | MAPK1 | 9.0x10-10 | 0.39 |
| rs2043732 | 7 | 51,192,161 | 0.06 | COBL | RASA2 | 1.3x10-9 | 0.050 |
| rs114617777 | 6 | 88,085,754 | 0.06 | SMIM8 / CFAP206 | SOS1 | 1.3x10-9 | 0.19 |
| chr13:78700408:D | 13 | 78,700,408 | 0.02 | EDNRB / POU4F1 | SPRED1 | 1.4x10-9 | 0.46 |
| rs72690923 | 1 | 106,012,196 | 0.03 | AMY1B / PRMT6 | BRAF | 1.4x10-9 | 0.66 |
| rs4128728 | 18 | 49,575,401 | 0.03 | MEX3C / DCC | SOS1 | 1.6x10-9 | 0.17 |
| rs11255742 | 10 | 8,598,746 | 0.03 | KRT8P16 | MAP2K1 | 1.6x10-9 | 0.087 |
| chr6:80625529:D | 6 | 80,625,529 | 0.13 | ELOVL4 | SHOC2 | 1.7x10-9 | 0.89 |
| rs73688732 | 7 | 31,068,898 | 0.02 | GHRHR / ADCYAP1R1 | MAP2K1 | 1.9x10-9 | 0.35 |
| rs1318299 | 2 | 220,283,259 | 0.02 | DES | BRAF | 2.1x10-9 | 0.47 |
| chr12:21624694:D | 12 | 21,624,694 | 0.10 | RECQL | SOS1 | 2.2x10-9 | 0.81 |
| rs73475884 | 13 | 35,080,882 | 0.07 | RFC3 / NBEA | SHOC2 | 2.2x10-9 | 0.28 |
| rs58413939 | 15 | 23,003,403 | 0.04 | CYFIP1 | RASA1 | 2.3x10-9 | 0.031 |
| rs143823697 | 5 | 134,412,896 | 0.03 | PITX1 / H2AFY | MAPK1 | 2.4x10-9 | 0.40 |
| rs12239450 | 1 | 47,933,492 | 0.09 | FOXD2 / TRABD2B | BRAF | 2.4x10-9 | 0.58 |
| rs113552799 | 6 | 123,947,624 | 0.04 | TRDN | MAP2K1 | 2.5x10-9 | 0.80 |
| rs254700 | 5 | 134,103,554 | 0.02 | DDX46 | SHOC2 | 2.6x10-9 | 0.37 |
| rs12582581 | 12 | 511,258 | 0.02 | CCDC77 | CBL | 2.6x10-9 | 0.26 |
| rs55942942 | 13 | 35,095,658 | 0.07 | RFC3 | SHOC2 | 2.7x10-9 | 0.29 |
| rs118078508 | 6 | 154,999,201 | 0.02 | CNKSR3 / SCAF8 | PTPN11 | 2.8x10-9 | 0.44 |