Table 2.
Top Transcript-SNP Pairs without a Significant Diagnosis Interaction
| Probe ID | Symbol | Chr. | Bp Position | Best SNP | S_Chr | S_Pos | Other | Loc. | Raw p Value | 1K p Value | Inter p Value | r2 CA | r2 CO | Dir. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GI_34147330-S | ABDH12 | 20 | 25.2–25.3 | rs4815412 | 20 | 25.3 | 40 | cis | 6.890 × 10−64 | 9.990 × 10−4 | 5.2030 × 10−2 | 0.43 | 0.38 | + |
| GI_8923854-A | AD-017 | 3 | 52.7 | rs1961958 | 3 | 52.6 | 31 | cis | 1.450 × 10−53 | 9.990 × 10−4 | 7.0820 × 10−1 | 0.34 | 0.32 | - |
| GI_22748838-S | AHSA2 | 2 | 61.3 | rs720201 | 2 | 61.2 | 19 | cis | 8.940 × 10−24 | 9.990 × 10−4 | 2.0130 × 10−1 | 0.25 | 0.13 | - |
| GI_14149802-S | ANKRD27 | 19 | 37.8–37.9 | rs438268 | 19 | 37.8 | 13 | cis | 1.840 × 10−36 | 9.990 × 10−4 | 1.3840 × 10−1 | 0.23 | 0.31 | + |
| GI_23238227-S | CHST7 | X | 46.3 | rs760697 | X | 46.3 | 3 | cis | 1.890 × 10−23 | 9.990 × 10−4 | 3.374 × 10−1 | 0.23 | 0.19 | + |
| GI_25306276-S | EFG1 | 3 | 159.8–159.9 | rs9832803 | 3 | 159.9 | 7 | cis | 1.420 × 10−34 | 9.990 × 10−4 | 5.860 × 10−1 | 0.29 | 0.20 | - |
| GI_31542792-S | FN3K | 17 | 78.3 | rs11078015 | 17 | 78.4 | 16 | cis | 3.130 × 10−79 | 9.990 × 10−4 | 6.905 × 10−1 | 0.48 | 0.45 | + |
| GI_24431963-S | HBS1L | 6 | 135.3–135.4 | rs4646871 | 6 | 135.3 | 15 | cis | 1.080 × 10−27 | 9.990 × 10−4 | 7.053 × 10−1 | 0.24 | 0.19 | - |
| GI_37059782-S | KIAA0980 | 20 | 25.4–25.5 | rs2258719 | 20 | 25.2 | 35 | cis | 1.860 × 10−28 | 9.990 × 10−4 | 5.377 × 10−2 | 0.27 | 0.17 | + |
| GI_21314694-S | KIAA1449 | 3 | 39.1 | rs811971 | 3 | 39.1 | 22 | cis | 5.080 × 10−39 | 9.990 × 10−4 | 2.428 × 10−1 | 0.31 | 0.27 | + |
| GI_41393558-I | KIF1B | 1 | 10.2–10.4 | rs10492972 | 1 | 10.3 | 22 | cis | 1.650 × 10−66 | 9.990 × 10−4 | 8.820 × 10−2 | 0.43 | 0.40 | - |
| GI_4826813-A | KTN1 | 14 | 55.1–55.2 | rs10137340 | 14 | 55.1 | 4 | cis | 2.650 × 10−23 | 4.995 × 10−3 | 2.312 × 10−1 | 0.12 | 0.21 | - |
| GI_24308385-S | LOC115294 | 8 | 52.9 | rs17212214 | 8 | 53 | 21 | cis | 2.020 × 10−28 | 9.990 × 10−4 | 7.537 × 10−1 | 0.24 | 0.20 | - |
| GI_37546921-S | LOC339804 | 2 | 61.2 | rs720201 | 2 | 61.2 | 13 | cis | 1.590 × 10−25 | 9.990 × 10−4 | 2.113 × 10−1 | 0.25 | 0.15 | + |
| GI_40786403-S | LOC374969 | 1 | 43.0–43.1 | rs323720 | 1 | 43 | 12 | cis | 6.260 × 10−37 | 9.990 × 10−4 | 4.611 × 10−1 | 0.26 | 0.31 | + |
| GI_28603839-S | MGC10120 | 10 | 102 | rs6584356 | 10 | 102 | 3 | cis | 9.020 × 10−37 | 1.998 × 10−3 | 7.180 × 10−2 | 0.27 | 0.26 | - |
| GI_33859747-S | MGC2752 | 19 | 63.8 | rs10413586 | 19 | 63.8 | 1 | cis | 3.940 × 10−32 | 9.990 × 10−4 | 3.401 × 10−1 | 0.23 | 0.23 | - |
| GI_31652223-A | MRPL21 | 11 | 68.4 | rs478647 | 11 | 68.5 | 10 | cis | 1.850 × 10−35 | 9.990 × 10−4 | 2.100 × 10−1 | 0.31 | 0.19 | - |
| GI_28872733-I | MRPL43 | 10 | 102.7 | rs4917916 | 10 | 102.7 | 5 | cis | 1.520 × 10−23 | 9.990 × 10−4 | 6.832 × 10−1 | 0.22 | 0.18 | - |
| GI_29826284-A | MRPL47 | 3 | 180.8 | rs10513762 | 3 | 180.8 | 2 | cis | 1.750 × 10−25 | 9.990 × 10−4 | 4.383 × 10−1 | 0.23 | 0.12 | - |
| GI_6912539-S | NUBP2 | 16 | 1.8 | rs3848348 | 16 | 1.8 | 18 | cis | 9.170 × 10−31 | 9.990 × 10−4 | 7.720 × 10−1 | 0.20 | 0.24 | + |
| GI_40288186-A | PDLIM2 | 8 | 22.5 | rs2291232 | 8 | 22.5 | 11 | cis | 8.470 × 10−43 | 9.990 × 10−4 | 6.109 × 10−1 | 0.25 | 0.31 | - |
| GI_30179910-A | PILRB | 7 | 99.8 | rs1000215 | 7 | 99.4 | 6 | cis | 4.330 × 10−28 | 9.990 × 10−4 | 9.318 × 10−1 | 0.24 | 0.18 | + |
| GI_31881619-A | PPA2 | 4 | 106.5–106.6 | a-1897043 | 4 | 106.5 | 19 | cis | 3.770 × 10−28 | 9.990 × 10−4 | 8.078 × 10−1 | 0.22 | 0.20 | - |
| GI_19557635-A | PPIL3 | 2 | 201.4–201.5 | rs10205561 | 2 | 201.5 | 14 | cis | 2.210 × 10−32 | 9.990 × 10−4 | 6.970 × 10−1 | 0.29 | 0.19 | - |
| GI_28274698-S | RAB3IP | 12 | 68.4–68.5 | rs11177823 | 12 | 68.4 | 3 | cis | 1.280 × 10−44 | 9.990 × 10−4 | 1.424 × 10−1 | 0.34 | 0.26 | - |
| GI_14149701-S | RNF167 | 17 | 4.8 | rs238237 | 17 | 4.4 | 4 | cis | 2.600 × 10−29 | 9.990 × 10−4 | 1.721 × 10−1 | 0.32 | 0.14 | + |
| GI_4506738-S | RPS6KB2 | 11 | 67 | rs1476792 | 11 | 67 | 2 | cis | 1.990 × 10−21 | 9.990 × 10−4 | 5.155 × 10−2 | 0.25 | 0.09 | - |
| GI_34147665-S | STK25 | 2 | 242.1 | rs3755400 | 2 | 242 | 1 | cis | 2.170 × 10−31 | 9.990 × 10−4 | 6.325 × 10−1 | 0.25 | 0.23 | - |
| GI_6912707-S | TIMM10 | 11 | 57.1 | rs2729371 | 11 | 57.1 | 6 | cis | 1.590 × 10−72 | 9.990 × 10−4 | 2.506 × 10−1 | 0.42 | 0.40 | - |
| GI_15451941-S | UBA52 | 19 | 18.5 | rs1468475 | 19 | 18.5 | 6 | cis | 3.550 × 10−81 | 9.990 × 10−4 | 3.116 × 10−1 | 0.43 | 0.46 | + |
| GI_4557872-S | UROS | 10 | 127.5 | rs1571278 | 10 | 127.5 | 14 | cis | 7.880 × 10−28 | 9.990 × 10−4 | 9.659 × 10−1 | 0.20 | 0.21 | - |
| GI_37622342-A | ZNF266 | 19 | 9.4 | rs4804436 | 19 | 9.4 | 23 | cis | 6.870 × 10−44 | 9.990 × 10−4 | 5.462 × 10−1 | 0.33 | 0.26 | - |
This table lists transcript and SNP pairs that had transcript-specific empirically significant p values by our 2 df model and where there was a nonsignificant diagnosis interaction term. Criteria for selection of the subset is as described in Table 1, except that the SNP had to account for greater than 20% of the variance in transcript expression in either cases or controls. The full data set is available in Table S6. All headers are as described in Table 1.