Table 4.
Results from Combined Meta-analysis on Non-LS–associated SNPs at Significance Meta-P Less Than 5 × 10−8 (Top 25 Findings)
| SNP | CHR | BP | CA/NCA | Gene (Nearby Genes) | SNP Location | Cohorts | Fixed-Effects Model |
Random-Effects Model |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) | Meta-P Value | OR (95% CI) | Meta-P Value | τ2P Value | I2 (%) | |||||||
| rs1964995 | 6 | 32557389 | G/A | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 0.60 (0.55–0.65) | 2.53E-32 | 0.61 (0.54–0.68) | 5.99E-17 | 1.55E-01 | 41.79 |
| rs2213585 | 6 | 32521128 | G/A | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 1.51 (1.39–1.63) | 8.82E-23 | 1.51 (1.34–1.70) | 3.36E-11 | 1.11E-01 | 54.69 |
| rs2227139 | 6 | 32521437 | G/A | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 1.50 (1.39–1.63) | 8.96E-23 | 1.51 (1.33–1.70) | 6.87E-11 | 1.03E-01 | 56.15 |
| rs2213586 | 6 | 32521072 | A/G | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 1.50 (1.38–1.63) | 1.29E-22 | 1.50 (1.33–1.70) | 4.58E-11 | 1.09E-01 | 54.98 |
| rs7192 | 6 | 32519624 | A/C | HLA-DRA | Coding | SWE, GER, USA-AA | 1.50 (1.39–1.63) | 1.31E-22 | 1.51 (1.34–1.69) | 8.78E-12 | 1.27E-01 | 51.57 |
| rs2395153 | 6 | 32453573 | C/G | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 0.63 (0.58–0.69) | 1.76E-22 | 0.63 (0.58–0.69) | 1.76E-22 | 5.17E-01 | 0.00 |
| rs7195 | 6 | 32520517 | A/G | HLA-DRA | UTR | SWE, GER, USA-AA | 1.50 (1.38–1.63) | 1.77E-22 | 1.50 (1.34–1.68) | 9.57E-13 | 1.52E-01 | 46.70 |
| rs3763327 | 6 | 32521808 | G/C | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, USA-AA | 1.57 (1.42–1.73) | 7.36E-19 | 1.57 (1.34–1.85) | 2.75E-08 | 1.08E-01 | 61.20 |
| rs477515 | 6 | 32677669 | A/G | (HLA-DRB1, HLA-DQA1) | Intergenic | SWE, GER, USA-AA | 0.64 (0.58–0.71) | 3.93E-18 | 0.63 (0.54–0.75) | 5.32E-08 | 7.79E-02 | 61.89 |
| rs2395182 | 6 | 32521295 | C/A | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 1.49 (1.36–1.62) | 7.05E-18 | 1.47 (1.22–1.78) | 4.95E-05 | 1.48E-02 | 76.86 |
| rs4373382 | 6 | 32458846 | C/A | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 0.69 (0.63–0.75) | 1.17E-17 | 0.69 (0.62–0.76) | 5.81E-13 | 2.48E-01 | 28.87 |
| rs3129952 | 6 | 32467741 | C/G | (C6orf10, BTNL2) | Intergenic | SWE, USA-AA | 1.64 (1.46–1.84) | 1.54E-17 | 1.64 (1.46–1.84) | 1.54E-17 | 4.18E-01 | 0.00 |
| rs4424066 | 6 | 32462406 | G/A | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 0.69 (0.63–0.75) | 1.73E-17 | 0.69 (0.62–0.76) | 3.44E-12 | 2.28E-01 | 32.82 |
| rs2076529 | 6 | 32471933 | G/A | BTNL2 | Coding | SWE, GER, USA-AA | 0.69 (0.63–0.75) | 1.74E-17 | 0.69 (0.62–0.76) | 1.70E-12 | 2.37E-01 | 30.92 |
| rs3817973 | 6 | 32469089 | A/G | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 0.69 (0.63–0.75) | 1.96E-17 | 0.69 (0.62–0.76) | 2.39E-12 | 2.34E-01 | 31.62 |
| rs2239802 | 6 | 32519824 | C/G | HLA-DRA | Intron | SWE, GER, USA-AA | 1.48 (1.35–1.61) | 1.97E-17 | 1.46 (1.22–1.76) | 5.85E-05 | 1.56E-02 | 76.65 |
| rs9268472 | 6 | 32463583 | A/G | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 0.69 (0.63–0.75) | 3.84E-17 | 0.69 (0.62–0.77) | 3.06E-11 | 2.04E-01 | 37.34 |
| rs3177928 | 6 | 32520413 | A/G | HLA-DRA | UTR | SWE, GER, USA-AA | 0.53 (0.46–0.62) | 8.37E-17 | 0.53 (0.46–0.62) | 8.37E-17 | 6.77E-01 | 0.00 |
| rs2076530 | 6 | 32471794 | G/A | BTNL2 | Coding | SWE, GER, USA-AA | 0.69 (0.64–0.76) | 1.21E-16 | 0.69 (0.64–0.76) | 1.21E-16 | 4.96E-01 | 0.00 |
| rs9268969 | 6 | 32542327 | A/G | (HLA-DRA, HLA-DRB5) | Intergenic | SWE, GER, USA-AA | 0.66 (0.60–0.73) | 1.29E-16 | 0.66 (0.60–0.73) | 1.29E-16 | 6.60E-01 | 0.00 |
| rs3129888 | 6 | 32519704 | G/A | HLA-DRA | Intron | SWE, GER, USA-AA | 1.48 (1.35–1.62) | 2.07E-16 | 1.47 (1.25–1.74) | 6.22E-06 | 4.00E-02 | 68.94 |
| rs3129948 | 6 | 32462622 | C/A | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 1.44 (1.32–1.58) | 2.30E-16 | 1.44 (1.27–1.63) | 1.46E-08 | 1.31E-01 | 50.83 |
| rs2294878 | 6 | 32475773 | A/C | BTNL2 | Intron | SWE, GER, USA-AA | 0.70 (0.64–0.76) | 3.66E-16 | 0.70 (0.64–0.76) | 3.66E-16 | 9.24E-01 | 0.00 |
| rs3117098 | 6 | 32466491 | G/A | (C6orf10, BTNL2) | Intergenic | SWE, GER, USA-AA | 1.44 (1.32–1.57) | 6.96E-16 | 1.43 (1.28–1.60) | 4.11E-10 | 2.01E-01 | 38.74 |
| rs3129961 | 6 | 32486918 | G/A | (BTNL2, HLA-DRA) | Intergenic | SWE, GER, USA-AA | 1.43 (1.31–1.56) | 1.02E-15 | 1.43 (1.28–1.60) | 6.67E-10 | 1.95E-01 | 39.66 |
Definition of abbreviations: BP = base pairs; CA = coded allele; CHR = chromosome; CI = confidence interval; GER = Germany; LS = Löfgren’s syndrome; NCA = noncoded allele; OR = odds ratio; SNP = single-nucleotide polymorphism; SWE = Sweden; USA-AA = US African American; UTR = untranslated region.
The entire list of non-LS–associated SNPs is provided in Table E6.
The overall association estimates (OR) and 95% CI for non-LS–associated SNPs under fixed-effect and random-effect models, respectively.
τ2 P represents the P value significance for the amount of heterogeneity in the true log odds; the I2 statistic represents how much of the total variability in the effect size estimate can be attributed to heterogeneity among the true effects. Cohorts from SWE and GER are of European ancestry; the USA-AA cohort is of African ancestry.