TABLE 3.
The top tag-SNPs (PGC < 3.5 × 10–7) associated with non-LS males and females in Swedish, German, and USA-AA cohorts.
| Males | ||||||||||
| SNP | CHR | BP (hg19) | Alleles | RefSeq genes | Cohort | CA | CAF | OR | 95% CI | P GC |
| rs1049550 | 10 | 81,926,702 | A/G | ANXA11 | SWE | A | 0.2962 | 0.5231 | (0.4195, 0.6523) | 1.82E-08 |
| GER | A | 0.3845 | 0.7325 | (0.6281, 0.8543) | 3.63E-04 | |||||
| USA-AA | A | 0.1508 | 0.7724 | (0.5841, 1.0215) | 7.70E-02 | |||||
| rs2239802 | 6 | 32,411,846 | C/G | HLA-DRA | SWE | C | 0.3375 | 1.7790 | (1.4295, 2.214) | 4.52E-07 |
| GER | C | 0.2283 | 1.4480 | (1.2336, 1.6997) | 4.75E-05 | |||||
| USA-AA | C | 0.3321 | 1.5140 | (1.2288, 1.8655) | 1.41E-04 | |||||
| rs7197 | 6 | 32,412,580 | A/G | HLA-DRA | SWE | A | 0.2885 | 1.7610 | (1.4056, 2.2063) | 1.50E-06 |
| GER | A | 0.1901 | 1.4210 | (1.1976, 1.6862) | 2.96E-04 | |||||
| USA-AA | A | 0.2253 | 1.6350 | (1.2895, 2.0731) | 7.32E-05 | |||||
| rs1964995 | 6 | 32,449,411 | G/A | 36kb 3′ of HLA-DRB5 | SWE | G | 0.2995 | 0.6033 | (0.4872, 0.747) | 5.74E-06 |
| GER | G | 0.3664 | 0.5452 | (0.464, 0.6406) | 3.40E-11 | |||||
| USA-AA | G | 0.2314 | 0.5568 | (0.431, 0.7194) | 1.21E-05 | |||||
| rs3830135 | 6 | 32,548,464 | A/G | HLA-DRB1 | SWE | A | 0.0529 | 0.3543 | (0.2278, 0.5512) | 6.71E-06 |
| GER | A | 0.0980 | 0.4374 | (0.3212, 0.5956) | 2.40E-06 | |||||
| USA-AA | C | 0.0702 | 0.5942 | (0.3897, 0.906) | 1.82E-02 | |||||
| rs3131283 | 6 | 32,119,898 | A/G | 177bp 5′ of PRRT1 | SWE | A | 0.1971 | 1.8100 | (1.4054, 2.3312) | 6.85E-06 |
| GER | A | 0.1417 | 1.3790 | (1.1382, 1.6707) | 3.21E-03 | |||||
| USA-AA | C | 0.0256 | 1.7040 | (0.9263, 3.1348) | 9.41E-02 | |||||
| rs4530903 | 6 | 32,581,889 | A/G | 23kb 5′ of HLA-DQA1 | SWE | A | 0.0529 | 0.3590 | (0.2308, 0.5585) | 8.79E-06 |
| GER | A | 0.0973 | 0.4282 | (0.3133, 0.5853) | 1.74E-06 | |||||
| USA-AA | T | 0.0702 | 0.5942 | (0.3897, 0.906) | 1.82E-02 | |||||
| rs1800684 | 6 | 32,151,994 | T/A | AGER | SWE | T | 0.1982 | 1.7920 | (1.3917, 2.3076) | 9.75E-06 |
| GER | A | 0.1428 | 1.3810 | (1.1401, 1.6729) | 3.00E-03 | |||||
| USA-AA | A | 0.0293 | 1.6280 | (0.9369, 2.8289) | 9.13E-02 | |||||
| rs3104402 | 6 | 32,681,676 | A/C | 27kb 5′ of HLA-DQA2 | SWE | A | 0.1050 | 2.0860 | (1.5013, 2.8984) | 1.83E-05 |
| GER | T | 0.0689 | 1.3750 | (1.0539, 1.794) | 3.50E-02 | |||||
| USA-AA | G | 0.0153 | 2.3790 | (1.0553, 5.3629) | 4.12E-02 | |||||
| rs1044506 | 6 | 32,172,065 | A/C | NOTCH4 | SWE | A | 0.2016 | 1.7870 | (1.3878, 2.3011) | 1.08E-05 |
| GER | T | 0.1441 | 1.3560 | (1.1203, 1.6413) | 4.97E-03 | |||||
| USA-AA | G | 0.0263 | 1.9640 | (1.0695, 3.6067) | 3.35E-02 | |||||
| Females | ||||||||||
| rs1964995 | 6 | 32,449,411 | G/A | 36kb 3′ of HLA-DRB5 | SWE | G | 0.2995 | 0.5314 | (0.4202, 0.6721) | 6.73E-07 |
| GER | G | 0.3611 | 0.5942 | (0.519, 0.6804) | 1.65E-12 | |||||
| USA-AA | G | 0.2408 | 0.8051 | (0.6963, 0.9309) | 3.77E-03 | |||||
| rs3129727 | 6 | 32,679,690 | A/G | 29kb 5′ of HLA-DQA2 | SWE | A | 0.0474 | 3.0760 | (2.0025, 4.7251) | 1.37E-06 |
| GER | A | 0.0268 | 1.9580 | (1.3773, 2.7836) | 4.53E-04 | |||||
| USA-AA | T | 0.0217 | 1.6270 | (1.0686, 2.4773) | 2.47E-02 | |||||
| rs3998158 | 6 | 32,681,992 | G/A | 27kb 5′ of HLA-DQA2 | SWE | G | 0.1700 | 0.5047 | (0.3771, 0.6755) | 1.49E-05 |
| GER | C | 0.1990 | 0.5811 | (0.4908, 0.6881) | 3.67E-09 | |||||
| USA-AA | C | 0.1665 | 1.0890 | (0.925, 1.2821) | 3.10E-01 | |||||
| rs2395153 | 6 | 32,345,595 | C/G | 5.9kb 5′ of C6orf10 | SWE | C | 0.2748 | 0.5947 | (0.4694, 0.7535) | 5.05E-05 |
| GER | C | 0.3391 | 0.6137 | (0.5347, 0.7044) | 7.74E-11 | |||||
| USA-AA | G | 0.2175 | 0.7410 | (0.6372, 0.8618) | 1.18E-04 | |||||
| rs2076529 | 6 | 32,363,955 | G/A | BTNL2 | SWE | G | 0.3176 | 0.6105 | (0.4859, 0.7672) | 6.66E-05 |
| GER | C | 0.3752 | 0.6458 | (0.5659, 0.7371) | 1.22E-09 | |||||
| USA-AA | C | 0.3056 | 0.8406 | (0.7363, 0.9598) | 1.11E-02 | |||||
| rs9268472 | 6 | 32,355,605 | A/G | 6.9kb 3′ of BTNL2 | SWE | A | 0.3176 | 0.6107 | (0.486, 0.7674) | 6.71E-05 |
| GER | T | 0.3754 | 0.6446 | (0.5648, 0.7357) | 1.04E-09 | |||||
| USA-AA | A | 0.3063 | 0.8471 | (0.7421, 0.967) | 1.51E-02 | |||||
| rs9275580 | 6 | 32,679,462 | G/A | 30kb 5′ of HLA-DQA2 | SWE | G | 0.1791 | 0.5543 | (0.4192, 0.7329) | 9.63E-05 |
| GER | C | 0.2102 | 0.5519 | (0.4666, 0.6528) | 7.77E-11 | |||||
| USA-AA | G | 0.2458 | 1.1700 | (1.0138, 1.3503) | 3.35E-02 | |||||
| rs3129882 | 6 | 32,409,530 | G/A | HLA-DRA | SWE | G | 0.5146 | 1.5580 | (1.263, 1.922) | 9.81E-05 |
| GER | G | 0.4499 | 1.1700 | (1.0356, 1.322) | 1.85E-02 | |||||
| USA-AA | A | 0.4586 | 1.0660 | (0.9446, 1.203) | 3.05E-01 | |||||
SNP, single nucleotide polymorphism; BP, chromosome base pairs are based on human genome assembly version 19 (hg19); CA, coded allele; CAF, coded allele frequency; OR, odds ratio; SE, standard error of odds ratio; PGC, genomic controlled P-value.