Table 2. Column 1 lists the 25 cis–trans interacting transcripts listed in GWAS catalog; column 3 lists the observed two-locus P-values; the remaining columns provide information concerning the cis- and trans-SNPs.
| Two-locus | Top cis-acting SNP | Top trans-acting SNP | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Transcripta | Disease (GWAS catalog) | P-value | rs | Chr | Position | rs | Chr | Position | RefSeq genes |
| ELMO1 | QT interval26 | 1.09E-10 | rs10259008 | 7 | 36 799 785 | rs776692 | 15 | 40 134 818 | PLA2G4D, PLA2G4E |
| NIN | Cognitive performance30 | 1.13E-10 | rs11850904 | 14 | 51 130 033 | rs6836445 | 4 | 29 296 175 | — |
| ZFP64 | Amyotrophic lateral sclerosis31 | 1.90E-09 | rs4811201 | 20 | 49 629 361 | rs6561342 | 13 | 46 458 623 | HTR2A, GNG5P5 |
| GORASP2 | Cognitive performance32 | 2.15E-09 | rs10930438 | 2 | 171 315 117 | rs17081840 | 4 | 55 718 936 | KDR |
| VRK2 | Schizophrenia33 | 2.16E-09 | rs10178765 | 2 | 58 363 538 | rs4950076 | 1 | 95 349 885 | ALG14, TMEM56 |
| SYNE1 | Blood pressure34 | 2.23E-09 | rs1856057 | 6 | 152 109 562 | rs6445296 | 3 | 62 678 612 | CADPS |
| C6orf106 | Height35, 36 | 2.52E-09 | rs3800341 | 6 | 33 972 976 | rs17105347 | 14 | 36 335 202 | SLC25A21 |
| JAK2 | Inflammatory bowel disease37, 38 | 3.40E-09 | rs10974793 | 9 | 4 793 651 | rs12475354 | 2 | 77 441 949 | LRRTM4 |
| WDR1 | Serum urate (cardiovascular disease)39, 40 | 3.53E-09 | rs7660895 | 4 | 9 594 543 | rs10085762 | 7 | 135 220 728 | — |
| CXXC1 | Chronic lymphocytic leukemia41 | 3.63E-09 | rs1705521 | 18 | 45 955 763 | rs11836262 | 12 | 8 772 935 | FAM80B |
| AP1B1 | Carotid atherosclerosis42 | 3.83E-09 | rs4822998 | 22 | 27 690 297 | rs2753596 | 14 | 38 712 591 | TRAPPC6B |
| ST6GAL1 | Drug-induced liver injury43 | 4.11E-09 | rs3872724 | 3 | 188 223 915 | rs1959205 | 14 | 43 877 663 | YWHAZP1 |
| PEX1 | Height44 | 4.66E-09 | rs2285504 | 7 | 92 825 257 | rs7034789 | 9 | 6 935 423 | JMJD2C |
| EXT1 | Height45 | 4.95E-09 | rs7006088 | 8 | 119 720 982 | rs6696976 | 1 | 97 701 564 | DPYD |
| BLK | Systemic lupus erythematosus22, 24, 25, rheumatoid arthritis23 | 5.30E-09 | rs1293320 | 8 | 11 729 348 | rs1634506 | 17 | 31 449 476 | CCL3, CCL4 |
| WDR36 | Plasma eosinophil count (asthma)46 | 5.47E-09 | rs27409 | 5 | 111 459 912 | rs9504183 | 6 | 4 605 997 | — |
| FNTB | Mean corpuscular volume47 | 5.96E-09 | rs1679880 | 14 | 64 723 379 | rs7165654 | 15 | 56 627 331 | LIPC |
| TSR1 | Aortic root size48 | 6.70E-09 | rs1109303 | 17 | 1 350 227 | rs1334751 | 10 | 29 057 579 | BAMBI |
| PRDM1 | Systemic lupus erythematosus24 | 7.23E-09 | rs1891720 | 6 | 107 259 564 | rs2993312 | 13 | 112 731 466 | MCF2L |
| MBD1 | Chronic lymphocytic leukemia41 | 8.44E-09 | rs1705521 | 18 | 45 955 763 | rs11836262 | 12 | 8 772 935 | FAM80B |
| METTL1 | Multiple sclerosis49 | 8.68E-09 | rs1908536 | 12 | 57 124 955 | rs4833611 | 4 | 120 366 908 | USP53 |
| LSP1 | Breast cancer50 | 8.91E-09 | rs2301160 | 11 | 1 053 767 | rs10930873 | 2 | 152 549 752 | CACNB4 |
| LDLR | Myocardial infarction51, LDL cholesterol52, 53, 54 | 9.08E-09 | rs11085720 | 19 | 10 178 763 | rs6445704 | 3 | 54 614 308 | CACNA2D3 |
| STAT2 | Psoriasis27 | 1.20E-08 | rs4495925 | 12 | 55 554 383 | rs10489631 | 1 | 67 373 703 | IL23R |
| UBE2L3 | Systemic lupus erythematosus24 | 4.29E-08 | rs165846 | 22 | 19 254 028 | rs5751963 | 22 | 23 462 498 | PIWIL3 |
a
Illumina probe Ids are available upon request.