Table 3.
Results from Combined Meta-analysis on 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 | |||||||
| rs3130288 | 6 | 32203979 | A/C | CREBL1 | 3′ UTR | GER, SWE | 4.16 (3.54–4.90) | 4.30E-66 | 4.16 (3.54–4.90) | 4.30E-66 |
| rs3129927 | 6 | 32441805 | C/A | C6orf10 | Intron | GER, SWE | 4.04 (3.36–4.84) | 1.29E-50 | 4.04 (3.36–4.84) | 1.29E-50 |
| rs9268219 | 6 | 32392086 | C/A | C6orf10 | Intron | GER, SWE | 4.05 (3.37–4.87) | 1.51E-50 | 4.05 (3.37–4.87) | 1.51E-50 |
| rs3129950 | 6 | 32466179 | C/G | (C6orf10, BTNL2) | Intergenic | GER, SWE | 4.06 (3.38–4.88) | 1.79E-50 | 4.06 (3.38–4.88) | 1.79E-50 |
| rs2395149 | 6 | 32433540 | A/G | C6orf10 | Intron | GER, SWE | 3.98 (3.32–4.77) | 3.55E-50 | 3.98 (3.32–4.77) | 3.55E-50 |
| rs3135394 | 6 | 32516475 | G/A | HLA-DRA | Intron | GER, SWE | 3.92 (3.27–4.70) | 7.66E-50 | 3.92 (3.27–4.70) | 7.66E-50 |
| rs1265757 | 6 | 32410360 | A/G | C6orf10 | Intron | GER, SWE | 3.97 (3.31–4.77) | 8.02E-50 | 3.97 (3.31–4.77) | 8.02E-50 |
| rs9268235 | 6 | 32398186 | A/G | C6orf10 | Intron | GER, SWE | 3.97 (3.31–4.76) | 8.22E-50 | 3.97 (3.31–4.76) | 8.22E-50 |
| rs7775397 | 6 | 32369230 | C/A | C6orf10 | Coding | GER, SWE | 3.94 (3.28–4.73) | 2.94E-49 | 3.94 (3.28–4.73) | 2.94E-49 |
| rs9268177 | 6 | 32382860 | A/C | C6orf10 | Intron | GER, SWE | 3.94 (3.28–4.73) | 2.98E-49 | 3.94 (3.28–4.73) | 2.98E-49 |
| rs2187668 | 6 | 32713862 | A/G | HLA-DQA1 | Intron | GER, SWE | 3.94 (3.28–4.73) | 3.29E-49 | 3.94 (3.28–4.73) | 3.29E-49 |
| rs389884 | 6 | 32048876 | G/A | STK19 | Intron | GER, SWE | 3.88 (3.24–4.65) | 4.28E-49 | 3.88 (3.24–4.65) | 4.28E-49 |
| rs3132971 | 6 | 32338234 | C/A | (NOTCH4, C6orf10) | Intergenic | GER, SWE | 3.93 (3.28–4.72) | 6.55E-49 | 3.93 (3.28–4.72) | 6.55E-49 |
| rs1794282 | 6 | 32774504 | A/G | (HLA-DQB1, HLA-DQA2) | Intergenic | GER, SWE | 3.92 (3.26–4.70) | 9.82E-49 | 3.92 (3.26–4.70) | 9.82E-49 |
| rs1150753 | 6 | 32167845 | G/A | TNXB | Intron | GER, SWE | 3.89 (3.25–4.67) | 1.26E-48 | 3.89 (3.25–4.67) | 1.26E-48 |
| rs3129716 | 6 | 32765414 | G/A | (HLA-DQB1, HLA-DQA2) | Intergenic | GER, SWE | 3.88 (3.23–4.65) | 1.77E-48 | 3.88 (3.23–4.65) | 1.77E-48 |
| rs2854275 | 6 | 32736406 | A/C | HLA-DQB1 | Intron | GER, SWE | 3.91 (3.25–4.69) | 2.39E-48 | 3.91 (3.25–4.69) | 2.39E-48 |
| rs2856674 | 6 | 32767623 | G/A | (HLA-DQB1, HLA-DQA2) | Intergenic | GER, SWE | 3.88 (3.24–4.66) | 2.80E-48 | 3.88 (3.24–4.66) | 2.80E-48 |
| rs3130490 | 6 | 31847099 | A/C | C6orf27 | Intron | GER, SWE | 3.82 (3.19–4.58) | 6.92E-48 | 3.82 (3.19–4.58) | 6.92E-48 |
| rs1270942 | 6 | 32026839 | G/A | CFB | Intron | GER, SWE | 3.79 (3.17–4.54) | 7.12E-48 | 3.79 (3.17–4.54) | 7.12E-48 |
| rs3132449 | 6 | 31733992 | A/G | (APOM, C6orf47) | Intergenic | GER, SWE | 3.76 (3.14–4.50) | 1.11E-47 | 3.76 (3.14–4.50) | 1.11E-47 |
| rs519417 | 6 | 31986412 | A/G | (ZBTB12, C2) | Intergenic | GER, SWE | 3.78 (3.16–4.52) | 1.34E-47 | 3.78 (3.16–4.52) | 1.34E-47 |
| rs497309 | 6 | 32000463 | C/A | (ZBTB12, C2) | Intergenic | GER, SWE | 3.78 (3.16–4.53) | 1.82E-47 | 3.78 (3.16–4.53) | 1.82E-47 |
| rs3117577 | 6 | 31835453 | G/A | MSH5 | Intron | GER, SWE | 3.76 (3.14–4.49) | 1.96E-47 | 3.76 (3.14–4.49) | 1.96E-47 |
| rs3117582 | 6 | 31728499 | C/A | (BAT3, APOM) | Intergenic | GER, SWE | 3.73 (3.12–4.46) | 2.53E-47 | 3.73 (3.12–4.46) | 2.53E-47 |
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; UTR = untranslated region.
The entire list of LS-associated SNPs is provided in Table E5.
The overall association estimates (OR) and 95% CI for LS-associated SNPs under fixed-effect and random-effect models, respectively. Cohorts from SWE and GER are of European ancestry.