Table 3.
Genetic variants associated with common autoimmune disease traits.
| Autoimmune disease trait | No. of SNPs reported in the GWAS catalogue reaching GWAS significance (P ≤ 5 × 10–8) and in linkage equilibrium | Average effect sizes (OR) of alleles | Largest discovery cohort’s sample size (ethnic population) | Largest replication cohort sample size (ethnic population) |
|---|---|---|---|---|
| Rheumatoid arthritis | 186 | 1.16 | 22,628 cases, 288,664 cases (European, East Asian) | 24,107 cases, 79,295 controls (East Asian, European) |
| Psoriasis | 127 | 1.75 | 11,988 cases, 275,335 controls (European) | 11,301 cases, 19,879 controls (European) |
| Crohn’s disease | 180 | 1.23 | 19,085 cases, 34,213 controls (European) | 16,619 cases, 31,766 controls (European, Iranian, Indian, East Asian) |
| Ulcerative colitis | 80 | 1.32 | 12,924 cases, 21,442 controls (European) | 25,683 cases, 17,015 controls (European) |
| Systemic lupus erythematosus | 184 | 1.41 | 11,590 cases, 15,984 controls (European, African American, Hispanic) | 1387 cases, 28,564 controls (Japanese) |
| Ankylosing spondylitis | 55 | 3.74 | 8726 cases, 34,213 controls (European) | 2111 cases, 4483 controls (European) |
| Autoimmune thyroid disease | 141 | 1.48 | 30,234 cases, 724,172 controls (European) | 7891 cases, 8351 controls (Han Chinese) |
| Coeliac disease | 59 | 1.29 | 11,489 cases, 22,308 controls (European) | 12,041 cases, 12,228 controls (European, Indian) |
| Type 1 diabetes | 66 | 1.30 | 9934 cases, 16,956 controls (European) | 4329 cases, 9543 controls (European) |
| Vitiligo | 70 | 1.37 | 2853 cases, 37,405 controls (European) | 6623 cases, 10,740 controls (East Asian) |
| Addison’s disease | 10 | 2.23 | 1223 cases, 4097 controls (European) | NA |
| Myasthenia gravis | 8 | 1.68 | 972 cases, 1977 controls (European) | 423 cases, 467 controls (European) |
| Steven Johnson’s Syndrome | 5 | 2.53 | 424 cases, 1881 controls (European) | 102 cases, 469 controls (East Asian, Indian, Brazilian) |
| Autoimmune hepatitis | 1 | 2.90 | 649 cases, 13,436 controls (European) | 451 cases, 4103 controls (European) |
Variants that reached GWAS significance (P ≤ 5 × 10–8) were identified from the GWAS catalogue from March–April 202137. The sample sizes of the largest discovery cohort used to identify the SNP at GWAS significance is provided. Where an independent validation cohort had also been used, details of the largest replication cohort are also provided. For a SNP to be included in this table, the following summary statistics had to be available: effect allele, non-effect allele, OR, and P-value (minimal statistics required for including a variant in a polygenic risk score). LD between the lead SNP in a region and any other SNPs in the region had to be <0.8. The average absolute OR of all SNPS associated with the relevant trait is reported.
GWAS genome-wide association study, OR odds ratio, NA not available, SNPs single nucleotide polymorphism.