Table 2.
Results of Immunochip Analysis on Non-LS versus Healthy Control Subjects Highlighting the Top 25 SNPs at Significance P Less Than 5 × 10−8
| SNP | CHR | BP | Gene (Nearby Genes) | CA/NCA | CAF | Discovery Cohort (Sweden, European Ancestry) (n = 2,750) |
Replicating Cohort (Germany, European Ancestry) (n = 4,911) |
Replicating Cohort (African American Ancestry) (n = 1,657) |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) | P Value | PGC | OR (95% CI) | P Value | OR (95% CI) | P Value | ||||||
| rs1964995 | 6 | 32557389 | (HLA-DRA, HLA-DRB5) | G/A | 0.296 | 0.55 (0.47–0.64) | 2.47E-15 | 2.57E-13 | 0.56 (0.48–0.66) | 1.19E-12 | 0.70 (0.59–0.82) | 1.95E-05 |
| rs9269110 | 6 | 32551247 | (HLA-DRA, HLA-DRB5) | A/C | 0.389 | 1.74 (1.51–2.01) | 5.78E-14 | 3.82E-12 | 1.34 (1.16–1.56) | 6.20E-05 | — | — |
| rs9269081 | 6 | 32549078 | (HLA-DRA, HLA-DRB5) | A/C | 0.376 | 1.71 (1.48–1.97) | 4.01E-13 | 2.01E-11 | 1.33 (1.14–1.54) | 1.63E-04 | — | — |
| rs6923504 | 6 | 32536164 | (HLA-DRA, HLA-DRB5) | G/C | 0.381 | 1.66 (1.44–1.91) | 4.05E-12 | 1.46E-10 | 1.35 (1.16–1.56) | 6.09E-05 | — | — |
| rs6903608 | 6 | 32536263 | (HLA-DRA, HLA-DRB5) | G/A | 0.381 | 1.66 (1.44–1.91) | 4.05E-12 | 1.46E-10 | 1.36 (1.17–1.57) | 3.55E-05 | — | — |
| rs9268882 | 6 | 32539601 | (HLA-DRA, HLA-DRB5) | A/G | 0.381 | 1.66 (1.44–1.91) | 4.54E-12 | 1.61E-10 | 1.36 (1.17–1.57) | 3.86E-05 | — | — |
| rs3998158 | 6 | 32789970 | (HLA-DQB1, HLA-DQA2) | G/A | 0.168 | 0.53 (0.45–0.64) | 5.35E-12 | 1.85E-10 | 0.60 (0.49–0.74) | 9.45E-07 | 1.19 (0.98–1.43) | 7.47E-02 |
| rs9275582 | 6 | 32788048 | (HLA-DQB1, HLA-DQA2) | A/G | 0.172 | 0.53 (0.45–0.64) | 5.56E-12 | 1.91E-10 | 0.59 (0.48–0.72) | 2.42E-07 | 1.29 (1.08–1.54) | 4.29E-03 |
| rs9275580 | 6 | 32787440 | (HLA-DQB1, HLA-DQA2) | G/A | 0.178 | 0.54 (0.46–0.65) | 9.71E-12 | 3.08E-10 | 0.60 (0.50–0.74) | 4.99E-07 | 1.42 (1.20–1.67) | 3.98E-05 |
| rs2395153 | 6 | 32453573 | (C6orf10, BTNL2) | C/G | 0.273 | 0.59 (0.51–0.69) | 1.46E-11 | 4.38E-10 | 0.68 (0.58–0.79) | 8.61E-07 | 0.63 (0.53–0.75) | 2.12E-07 |
| rs3129948 | 6 | 32462622 | (C6orf10, BTNL2) | C/A | 0.390 | 1.63 (1.41–1.88) | 4.11E-11 | 1.06E-09 | 1.35 (1.17–1.56 | 5.66E-05 | 1.35 (1.14–1.60) | 6.34E-04 |
| rs3117098 | 6 | 32466491 | (C6orf10, BTNL2) | G/A | 0.390 | 1.59 (1.38–1.84) | 2.37E-10 | 4.78E-09 | 1.35 (1.16–1.56) | 6.45E-05 | 1.36 (1.14–1.61) | 4.63E-04 |
| rs3129954 | 6 | 32473558 | BTNL2 | A/G | 0.390 | 1.59 (1.38–1.84) | 2.37E-10 | 4.78E-09 | 1.35 (1.16–1.56) | 6.10E-05 | 1.34 (1.13–1.59) | 8.91E-04 |
| rs4424066 | 6 | 32462406 | (C6orf10, BTNL2) | G/A | 0.314 | 0.62 (0.54–0.72) | 2.54E-10 | 5.06E-09 | 0.70 (0.60–0.81) | 3.09E-06 | 0.75 (0.64–0.87) | 1.97E-04 |
| rs3129961 | 6 | 32486918 | (BTNL2, HLA-DRA) | G/A | 0.390 | 1.59 (1.38–1.84) | 2.82E-10 | 5.53E-09 | 1.34 (1.16–1.55) | 7.52E-05 | 1.35 (1.14–1.60) | 4.18E-04 |
| rs3129955 | 6 | 32473818 | BTNL2 | A/G | 0.385 | 1.59 (1.38–1.84) | 3.49E-10 | 6.64E-09 | 1.35 (1.17–1.56) | 5.19E-05 | 1.34 (1.13–1.59) | 8.24E-04 |
| rs4373382 | 6 | 32458846 | (C6orf10, BTNL2) | C/A | 0.313 | 0.63 (0.54–0.73) | 4.16E-10 | 7.72E-09 | 0.69 (0.59–0.80) | 1.58E-06 | 0.75 (0.65–0.87) | 1.73E-04 |
| rs3817973 | 6 | 32469089 | (C6orf10, BTNL2) | A/G | 0.314 | 0.63 (0.54–0.73) | 4.35E-10 | 8.02E-09 | 0.69 (0.59–0.80) | 1.57E-06 | 0.75 (0.65–0.88) | 2.68E-04 |
| rs2076529 | 6 | 32471933 | BTNL2 | G/A | 0.314 | 0.63 (0.54–0.73) | 4.35E-10 | 8.02E-09 | 0.69 (0.59–0.80) | 1.48E-06 | 0.75 (0.65–0.88) | 2.56E-04 |
| rs9268472 | 6 | 32463583 | (C6orf10, BTNL2) | A/G | 0.314 | 0.63 (0.54–0.73) | 4.61E-10 | 8.43E-09 | 0.69 (0.59–0.80) | 1.57E-06 | 0.76 (0.65–0.89) | 4.44E-04 |
| rs9271588 | 6 | 32698931 | (HLA-DRB1, HLA-DQA1) | G/A | 0.351 | 0.64 (0.56–0.74) | 8.35E-10 | 1.40E-08 | 0.67 (0.58–0.78) | 2.40E-07 | — | — |
| rs2858332 | 6 | 32789139 | (HLA-DQB1, HLA-DQA2) | A/C | 0.354 | 0.65 (0.56–0.75) | 1.47E-09 | 2.28E-08 | 1.36 (1.18–1.57) | 3.07E-05 | — | — |
| rs3830135 | 6 | 32656442 | HLA-DRB1 | A/G | 0.054 | 0.42 (0.32–0.56) | 1.82E-09 | 2.74E-08 | 0.56 (0.42–0.74) | 3.16E-05 | — | — |
Definition of abbreviations: BP = base pairs; CA = coded allele; CAF = coded allele frequency; CHR = chromosome; CI = confidence interval; LS = Löfgren’s syndrome; NCA = noncoded allele; OR = odds ratio; P = unadjusted P value; PGC = adjusted P value by genomic control (lambda = 1.17); SNP = single-nucleotide polymorphism.
Genetic effects (OR) adjusted according to sex, coded allele. OR is the risk on LS (0/1) per allele based on the additive genetic model. 95% CI is the 95% CI for the OR.
The entire list of non-LS–associated SNPs is provided in Table E3.