Table 2 Top ranking SNPs identified from pooled genome wide association study and validation genotyping in the discovery cohort
From: Pooled genome wide association detects association upstream of FCRL3 with Graves’ disease
GWAS pooled genotyping (Cases = 412, Controls = 498) | Validation individual genotyping (Cases = 412, Controls = 480) | ||||||||
|---|---|---|---|---|---|---|---|---|---|
SNP name | Location chr and bp | Gene | A1 | P value | OR_A1 | F_A | F_U | P value* | OR_A1* (95 % CI) |
Rs9676286 | Chr19q13.43 58126481 | ZNF134 intron | A | 1.08 × 10−8 | 2.08 | 0.047 | 0.023 | 5.54 × 10−3 | 2.28 (1.27, 4.09) |
rs9644119 | Chr8p21.2 26517817 | DPYSL2 2124 bp downstream | T | 9.10 × 10-8 | 1.78 | 0.177 | 0.128 | 0.033 | 1.36 (1.03, 1.79) |
rs11722643 | Chr4p16.1 10127484 | Intergenic WDR1 upstream, ZNF518B downstream | T | 1.03 × 10−7 | 1.88 | 0.101 | 0.054 | 1.38 × 10−3 | 1.91 (1.28, 2.83) |
Rs686806 | Chr 11q22.3 107228533 | CWF19L2 intron | T | 2.36 × 10−7 | 1.70 | 0.242 | 0.168 | 9.6 × 10−4 | 1.53 (1.19, 1.97) |
rs62469516 | Chr7q21.13 88958624 | ZNF804B intron | A | 2.68 × 10−7 | 0.51 | 0.043 | 0.088 | 5.73 × 10−5 | 0.41 (0.26, 0.63) |
rs73452600 | Chr 7q34 142828104 | PIP 1070 bp upstream | A | 3.49 × 10−7 | 1.90 | 0.099 | 0.061 | 3.37 × 10−3 | 1.80 (1.22, 2.67) |
Rs1662312 | Chr 18p11.31 3220450 | MYOM1 upstream | A | 5.72 × 10−7 | 0.51 | 0.040 | 0.080 | 5.33 × 10−4 | 0.45 (0.29, 0.71) |
rs1469893 | Chr 15q14 34988664 | GJD2 56015 bp Downstream | A | 6.58 × 10−7 | 0.58 | 0.05 | 0.104 | 6.86 × 10−5 | 0.44 (0.29, 0.66) |
Rs17676303 | Chr 1q23.1 157679691 | FCRL3 9044 bp upstream | T | 8.05 × 10−7 | 1.68 | 0.254 | 0.150 | 1.14 × 10−8 | 2.05 (1.57, 2.67) |
rs28578508 | Chr18q12.1 32316007 | DTNA intron | A | 8.16 × 10−7 | 0.56 | 0.062 | 0.099 | 2.80 × 10−3 | 0.56 (0.39, 0.82) |
rs78542322 | Chr 6q14.1 77291670 | Intergenic IMPG1 upstream HTR1B downstream | T | 9.82 × 10−7 | 0.52 | 0.071 | 0.141 | 3.27 × 10−5 | 0.47 (0.33, 0.67) |
Rs3818779 | Chr 10q26.11 121140671 | GRK5 intron | A | 1.51 × −6 | 1.94 | 0.059 | 0.029 | 2.08 × 10−3 | 2.30 (1.35, 3.9) |
rs2141440 | Chr 11q14.3 90898463 | Intergenic MIR4490 and FAT3 | A | 4.48 × 10−6 | 0.58 | 0.078 | 0.097 | 0.34 | 0.84 (0.59, 1.20) |