Table 3.
Summary of top-ranking eGenes for noncoding psoriasis-associated MHC variants with a Bayesian posterior probability > 0.5
| Variant | Ancestry | PP | Nearest gene (position) | Top eGenesa | No. tissuesb | Distance to TSS (kb) | No. tissues with +, − risk allele effectc |
|
|---|---|---|---|---|---|---|---|---|
| Most significant eQTL | Significant eQTL | |||||||
| rs1655901 | EUR | 1.000 | HLA-A (3.1 kb downstream) | HLA-F-AS1 | 46 | 200.0 | 13, 0 | 23, 1 |
| HLA-A | 53 | 6.5 | 11, 0 | 13, 6 | ||||
| HLA-F | 40 | 225.6 | 0, 6 | 0, 15 | ||||
| rs2844626 | SAS+EUR | 0.541 | HLA-C (7.0 kb downstream) | CCHCR1 | 58 | 104.0 | 14, 0 | 29, 6 |
| HLA-C | 58 | 10.3 | 13, 0 | 35, 2 | ||||
| AL645933.2 0.2 | 43 | 133.7 | 0, 16 | 0, 27 | ||||
| rs72866766 | EUR | 1.000 | HLA-B (468 bp downstream) | MICA | 45 | 47.3 | 0, 22 | 0, 29 |
| HLA-C | 58 | 81.3 | 8, 1 | 10, 7 | ||||
| DDX39B | 58 | 188.6 | 5, 0 | 10, 0 | ||||
| rs137854633 | EUR | 0.543 | HLA-B (intron 1) | HLA-B | 31 | 0.1 | 0, 21 | 0, 29 |
| HLA-C | 44 | 85.0 | 0, 10 | 1, 29 | ||||
| MICB | 31 | 137.8 | 3, 0 | 15, 0 | ||||
| rs2853998 | SAS+EUR | 0.942 | HLA-B (2.2 kb upstream) | AL645933.2 | 40 | 36.1 | 0, 11 | 0, 22 |
| HLA-B | 40 | 2.2 | 0, 8 | 0, 35 | ||||
| HLA-C | 53 | 87.3 | 0, 7 | 3, 18 | ||||
| rs2442752 | SAS | 0.583 | AL671883.3 (7.9 kb downstream) | HLA-C | 58 | 111.9 | 11, 8 | 13, 18 |
| HLA-B | 45 | 26.8 | 5, 0 | 23, 0 | ||||
| PSORS1C3 | 48 | 173.1 | 4, 0 | 20, 0 | ||||
| rs6935999 | EUR | 0.752 | HLA-DRA (15 kb upstream) | HSPA1L | 44 | 609.3 | 0, 4 | 0, 9 |
| AGER | 44 | 240.7 | 3, 0 | 6, 0 | ||||
| HLA-DRB1 | 44 | 164.9 | 3, 0 | 5, 1 | ||||
| NCR3 | 37 | 831.2 | 0, 3 | 0, 3 | ||||
| rs4947340 | EUR | 0.965 | HLA-DRA (23 kb upstream) | HLA-DQA2 | 34 | 273.8 | 18, 0 | 33, 0 |
| HLA-DRB1 | 49 | 122.3 | 0, 14 | 0, 48 | ||||
| HLA-DQB2 | 33 | 296.0 | 6, 0 | 30, 1 | ||||
| rs9271539 | SAS+EUR | 0.562 | HLA-DQA1 (15 kb upstream) | HLA-DRB5 | 52 | 92.0 | 28, 0 | 49, 0 |
| HLA-DRB1 | 52 | 32.4 | 12,0 | 22, 4 | ||||
| HLA-DQA1 | 36 | 15.2 | 1, 1 | 8, 5 | ||||
| PSMB9 | 52 | 231.9 | 0, 2 | 0, 24 | ||||
Abbreviations: PP, posterior probability; eGene, gene whose expression is significantly associated with an eQTL; eQTL, expression quantitative trait locus; EUR, European; SAS, South Asian; TSS, transcription start site.
Expressed genes with a TSS within 1 Mb of the variant were ranked by the number of 58 psoriasis-relevant tissues for which the eQTL effects of that variant upon the gene were the most significant. The top three ranking eGenes are shown for each variant (four eGenes shown for two variants because of ties).
Number of 58 tissues from 16 RNA expression studies for which the eQTL effect of the variant on the eGene was assessed. See Table S37 for citations of the 16 expression studies.