Table 2.
MiRSNPs associated with autoimmune disease.
| miRSNP | chr | pos_bp(hg38) | Ref. allele | Minor allele | MAF | Disease | P-value | OR | Target gene | miRNA | Effect on miRNA | NBS | eQTL (effect direction) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs7559479 | 2 | 102452327 | A | G | 0.22 | Crohn's disease | 2.2e-10 | 1.15 | IL18RAP | hsa-miR-3156-3p | C | 0.79 | Yes (up) |
| Celiac disease | 1.4e-16 | 1.19 | hsa-miR-4301 | C | 0.86 | ||||||||
| Inflammatory bowel disease | NA | NA | hsa-miR-136 | C | 0.92 | ||||||||
| rs7603250 | 2 | 102452374 | A | T | 0.22 | Crohn's disease | 1.6e-10 | 0.8 | IL18RAP | hsa-miR-455-3p | C | 0.94 | Yes (up) |
| Inflammatory bowel disease | 1.8e-09 | 0.8 | |||||||||||
| Celiac disease | NA | NA | |||||||||||
| rs3732421 | 3 | 119431242 | A | G | 0.16 | Multiple sclerosis | 3.5e-12 | 0.85 | TMEM39A | hsa-miR-449b-3p | D | 0.72 | No |
| Primary biliary cirrhosis | 1.7e-11 | 0.72 | hsa-miR-4691-3p | D | 0.82 | ||||||||
| hsa-miR-449b | D | 0.92 | |||||||||||
| rs57271503 | 3 | 119525746 | G | A | 0.16 | Multiple sclerosis | 4.1e-15 | 0.84 | CD80 | hsa-miR-769-5p | C | 0.71 | No |
| Primary biliary cirrhosis | 9.4e-13 | 0.71 | hsa-miR-4802-5p | C | 0.80 | ||||||||
| hsa-miR-769-5p | C | 0.71 | |||||||||||
| rs1054037 | 4 | 102631552 | T | C | 0.49 | Primary biliary cirrhosis | 8.3e-10 | 0.82 | MANBA | hsa-miR-660 | D | 0.90 | Yes (down/up) |
| Multiple sclerosis | NA | NA | hsa-miR-5591-3p | D | 0.95 | ||||||||
| hsa-miR-660-5p | D | 0.82 | |||||||||||
| hsa-miR-7151-5p | C | 0.71 | |||||||||||
| hsa-miR-3686 | C | 0.94 | |||||||||||
| rs4013 | 4 | 102631656 | T | C | 0.51 | Primary biliary cirrhosis | NA | NA | MANBA | hsa-miR-4742-3p | C | 0.76 | Yes (down/up) |
| Multiple sclerosis | NA | NA | hsa-miR-4778-5p | C | 0.91 | ||||||||
| hsa-miR-630 | C | 0.82 | |||||||||||
| rs1054029 | 4 | 102631896 | A | G | 0.51 | Primary biliary cirrhosis | NA | NA | MANBA | hsa-miR-124-5p | D | 0.80 | Yes (down/up) |
| Multiple sclerosis | NA | NA | hsa-miR-4255 | D | 0.99 | ||||||||
| hsa-miR-4766-5p | D | 0.74 | |||||||||||
| hsa-miR-124 | D | 0.90 | |||||||||||
| hsa-miR-33a | D | 0.77 | |||||||||||
| rs39602 | 5 | 97028750 | G | C | 0.41 | Ankylosing spondylitis | NA | NA | LNPEP | hsa-miR-6800-5p | D | 0.99 | Yes (down) |
| Crohn's disease | 6.9e-11 | 1.1 | |||||||||||
| Juvenile idiopathic arthritis | NA | NA | |||||||||||
| rs2070197 | 7 | 128948946 | T | C | 0.1 | Systemic lupus erythematosus | 3.0e-40 | 1.7 | IRF5 | hsa-miR-3136-3p | D | 0.91 | Yes (up) |
| Primary biliary cirrhosis | 1.8e-18 | 1.5 | hsa-miR-7155-3p | D | 0.89 | ||||||||
| rs10114470 | 9 | 114785492 | C | T | 0.33 | Crohn's disease | 1.5e-15 | 1.1 | TNFSF15 | hsa-miR-376a-3p | D | 0.84 | Yes (up) |
| Inflammatory bowel disease | 1.5e-16 | 0.8 | hsa-miR-4753-5p | D | 0.74 | ||||||||
| rs3088081 | 9 | 136375697 | A | G | 0.42 | Inflammatory bowel disease | 1.9e-22 | 0.8 | SNAPC4 | hsa-miR-3661 | C | 0.80 | yes (down) |
| Crohn's disease | 2.1e-17 | 0.8 | |||||||||||
| Ulcerative colitis | 1.0e-11 | 0.8 | |||||||||||
| rs9943 | 13 | 39752145 | A | G | 0.34 | Juvenile idiopathic arthritis | NA | NA | COG6 | hsa-miR-628-5p | C | 0.98 | Yes (down) |
| Rheumatoid arthritis | NA | NA | |||||||||||
| rs3839999 | 13 | 99385548 | AT | A | 0.22 | Crohn's disease | NA | NA | UBAC2 | hsa-miR-365a-3p | C | 0.93 | No |
| Inflammatory bowel disease | NA | NA | |||||||||||
| rs907091 | 17 | 39765489 | C | T | 0.51 | Primary biliary cirrhosis | 1.0e-10 | 0.79 | IKZF3 | hsa-miR-4497 | D | 0.97 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-3649 | C | 0.85 | ||||||||
| Ulcerative colitis | 8.1e-09 | 0.8 | hsa-miR-4518 | C | 0.92 | ||||||||
| Inflammatory bowel disease | 3.3e-13 | 0.8 | hsa-miR-330-5p | C | 0.99 | ||||||||
| hsa-miR-518c | C | 0.86 | |||||||||||
| hsa-miR-4314 | C | 0.84 | |||||||||||
| hsa-miR-326 | C | 0.99 | |||||||||||
| hsa-miR-3192 | C | 0.73 | |||||||||||
| rs16940681 | 17 | 45834793 | G | C | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-6740-5p | D | 0.84 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | |||||||||||
| rs2316765 | 17 | 45835088 | T | C | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-3192 | D | 0.73 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-30c-2-3p | D | 0.97 | ||||||||
| hsa-miR-30c-1-3p | D | 0.90 | |||||||||||
| rs878886 | 17 | 45835124 | C | G | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-4685-5p | D | 0.96 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-1915-3p | D | 0.71 | ||||||||
| hsa-miR-3918 | D | 0.86 | |||||||||||
| hsa-miR-7160-3p | D | 0.76 | |||||||||||
| rs878887 | 17 | 45835216 | C | T | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-198 | C | 0.85 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-3186-5p | D | 0.88 | ||||||||
| hsa-miR-136 | C | 0.92 | |||||||||||
| rs878888 | 17 | 45835269 | A | G | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-5708 | C | 0.70 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-1226-5p | D | 0.72 | ||||||||
| rs4640231 | 17 | 45835420 | G | C | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-6841-5p | D | 0.81 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-6755-5p | D | 0.77 | ||||||||
| rs4482334 | 17 | 45835464 | T | C | 0.24 | Primary biliary cirrhosis | NA | NA | CRHR1 | hsa-miR-6890-5p | D | 0.93 | Yes (up) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-6742-5p | D | 0.94 | ||||||||
| hsa-miR-4722-5p | D | 0.77 | |||||||||||
| hsa-miR-6796-5p | D | 0.75 | |||||||||||
| hsa-miR-4459 | D | 0.80 | |||||||||||
| rs12373168 | 17 | 45846971 | A | C | 0.24 | Primary biliary cirrhosis | NA | NA | SPPL2C | hsa-miR-33b-3p | D | 0.87 | No |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-519e-3p | D | 0.87 | ||||||||
| rs60474474 | 18 | 12792737 | C | T | 0.14 | Inflammatory bowel disease | 1.4e-10 | 1.1 | PTPN2 | hsa-miR-4290 | D | 0.99 | No |
| Crohn's disease | 2.2e-12 | 1.2 | |||||||||||
| Type 1 diabetes mellitus | NA | NA | |||||||||||
| Celiac disease | NA | NA | |||||||||||
| Juvenile idiopathic arthritis | NA | NA | |||||||||||
| rs45450798 | 18 | 12792941 | C | G | 0.14 | Inflammatory bowel disease | 2.0e-10 | 0.8 | PTPN2 | hsa-miR-4531 | C | 0.73 | No |
| Crohn's disease | 2.9e-12 | 0.8 | |||||||||||
| Type 1 diabetes mellitus | NA | NA | |||||||||||
| Celiac disease | NA | NA | |||||||||||
| Juvenile idiopathic arthritis | NA | NA | |||||||||||
| rs9950174 | 18 | 69846569 | T | C | 0.53 | Psoriasis | NA | NA | CD226 | hsa-miR-5189-3p | D | 0.85 | Yes (up) |
| rs727088 | 18 | 69863203 | G | A | 0.53 | Inflammatory bowel disease | 4.6e-9 | 1.08 | CD226 | hsa-miR-513a-3p | D | 0.75 | Yes (up) |
| Ulcerative colitis | 1.9e-8 | 1.1 | hsa-miR-181c | D | 0.75 | ||||||||
| Psoriasis | NA | NA | |||||||||||
| rs571689 | 19 | 48704297 | C | T | 0.47 | Crohn's disease | 7.3e-09 | 1.1 | FUT2 | hsa-miR-648 | D | 0.89 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-552-3p | C | 0.92 | ||||||||
| rs570794 | 19 | 48704394 | T | C | 0.47 | Crohn's disease | 1.0e-08 | 0.8 | FUT2 | hsa-miR-4430 | D | 0.71 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-1295b-5p | C | 0.79 | ||||||||
| hsa-miR-4463 | C | 0.95 | |||||||||||
| hsa-miR-1912 | C | 0.94 | |||||||||||
| rs507766 | 19 | 48705286 | T | C | 0.47 | Crohn's disease | 1.4e-08 | 0.8 | FUT2 | hsa-miR-136-5p | C | 0.83 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | hsa-miR-675 | C | 0.80 | ||||||||
| hsa-miR-887 | C | 0.92 | |||||||||||
| hsa-miR-410 | C | 0.73 | |||||||||||
| hsa-miR-191 | C | 0.75 | |||||||||||
| rs506897 | 19 | 48705372 | G | C | 0.47 | Crohn's disease | 7.3e-09 | 1.1 | FUT2 | hsa-miR-4530 | C | 0.81 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | |||||||||||
| rs503279 | 19 | 48705753 | T | C | 0.47 | Crohn's disease | 6.7e-09 | 0.8 | FUT2 | hsa-miR-675-3p | C | 0.86 | Yes (down) |
| Type 1 diabetes mellitus | NA | NA | |||||||||||
| rs1056441 | 20 | 63738996 | C | T | 0.28 | Crohn's disease | 5.4e-11 | 0.8 | LIME1 | hsa-miR-4745-3p | C | 0.97 | Yes (down) |
| Inflammatory bowel disease | 1.5e-15 | 0.8 | hsa-miR-1538 | C | 0.97 | ||||||||
| hsa-miR-4467 | C | 0.87 | |||||||||||
| hsa-miR-6770-3p | C | 0.78 | |||||||||||
| hsa-miR-3940-3p | D | 0.82 | |||||||||||
| hsa-miR-762 | D | 0.94 | |||||||||||
| rs7444 | 22 | 21622645 | T | C | 0.2 | Systemic lupus erythematosus | 1.8e-22 | 1.27 | UBE2L3 | hsa-miR-4741 | D | 0.90 | Yes (up) |
| Crohn's disease | 1.3e-12 | 1.1 | hsa-miR-4763-3p | D | 0.89 | ||||||||
| Inflammatory bowel disease | 6.9e-10 | 0.8 | hsa-miR-3918 | D | 0.86 | ||||||||
| hsa-miR-1207-5p | D | 0.92 | |||||||||||
| rs7445 | 22 | 21622758 | C | T | 0.19 | Crohn's disease | 6.3e-09 | 1.1 | UBE2L3 | hsa-miR-3064-5p | C | 0.93 | Yes (up) |
| Inflammatory bowel disease | 3.5e-10 | 1.1 | |||||||||||
| Systemic lupus erythematosus | 1.0e-12 | 1.27 |
NA, P-value was not available in the source study but this miRSNP is in linkage disequilibrium (r2 ≥ 0.8) with the most associated SNP reported; P-value obtained from each study. Bold: reported as associated in the original study. C, creates a binding site; D, disrupts a binding site; chr, chromosome; MAF, global minor allele frequency from the 1000 Genomes project; up, upregulated effect; down, downregulated effect; pos_bp, position in base pair; OR, odds ratio. OR was calculated based on the minor allele of the respective variant; eQTL, expression quantitative trait locus; NBC, naïve Bayes combined score.