Table 1.
Cis- and trans-eQTLs detected in EAE spleen day 35 post-immunization
| Chr | Transcript |
EAE(a) | EAE(i) | |||
|---|---|---|---|---|---|---|
| cis | trans | cis | trans | cis | trans | |
| 1 | 123 (20) | 264 (12) | 106 (32) | 216 (69) | 80 (26) | 71 (15) |
| 2 | 69 | 196 | 51 | 142 | 35 | 46 |
| 3 | 23 | 20 | 19 | 15 | 17 | 18 |
| 4 | 64 (47) | 8 (6) | 62 (50) | 8 (6) | 59 (50) | 13 (7) |
| 5 | 7 | 17 | 6 | 13 | 9 | 20 |
| 6 | 45 | 71 | 39 (8) | 57 (4) | 37 (9) | 105 (14) |
| 7 | 14 (2) | 5 (1) | 13 (1) | 3 (1) | 8 | 6 (2) |
| 8 | 25 (9) | 12 (4) | 27 (2) | 24 | 26 (3) | 89 (3) |
| 9 | 11 | 4 | 11 | 6 | 8 | 8 |
| 10 | 21 (17) | 24 (20) | 20 (17) | 32 (29) | 14 (11) | 22 (21) |
| 11 | 14 | 35 | 13 | 45 | 24 | 509 |
| 12 | 10 | 11 (1) | 10 | 10 (1) | 10 | 9 |
| 13 | 14 (3) | 15 (5) | 13 (2) | 12 (2) | 11 (3) | 10 (1) |
| 14 | 13 (3) | 17 (2) | 10 (3) | 9 (3) | 9 (3) | 6 (2) |
| 15 | 38 | 49 | 32 | 31 | 24 | 8 |
| 16 | 31 | 172 | 25 | 74 | 25 | 258 |
| 17 | 28 (5) | 643 (141) | 24 (7) | 408 (102) | 10 (2) | 158 (31) |
| 18 | 14 | 20 | 13 | 17 | 5 | 7 |
| 19 | 15 | 56 | 13 | 44 | 11 | 34 |
| 20 | 4 | 34 | 5 | 38 | 3 | 14 |
| X | 16 | 13 | 17 | 9 | 15 | 16 |
| Total | 599 (106) | 1686 (192) | 529 (122) | 1213 (217) | 440 (107) | 1427 (96) |
Number of cis- and trans-regulated transcripts for each chromosome and total (rows) for a selection of clinical phenotypes as covariates (column pairs). eQTLs were selected to have a logarithm of odds score ≥ 2 (generated with the Haley–Knott regression model in R/qtl) and a genome-wide corrected P-value of ≤0.05 (generated with 1000 permutations). Numbers in parentheses refer to the subset of transcripts controlled by loci in EAE QTLs (see Supplementary Material, Table S5). Abbreviations: eQTL, expression quantitative trait locus; Chr, chromosome; Transcript, no covariate; EAE(a), incidence of EAE as covariate, additive model; EAE(i), incidence of EAE as covariate, interactive model.