Table 2 Top SNPs in the combined analysis of the GWAS and the replication study
From: Genome-wide association and replication study of anti-tuberculosis drugs-induced liver toxicity
SNP | Chr (loci) | Alleles (RA) | Study | Cases/controls | MAF | P_min | P_adj | OR (95Â % CI) | Nearest gene |
|---|---|---|---|---|---|---|---|---|---|
rs10946737 | 6 (24967240) | A/G (A) | GWAS | 48/354 | 0.10 | 2.0 × 10−5 | 9.7 × 10−6 | 4.3 (2.5–7.4) | FAM65B |
Rep | 27/216 | 0.10 | 3.8 × 10−2 | 8.6 × 10−2 | 2.2 (0.9–5.4) | ||||
Comb | 75/570 | 0.10 | 6.3 × 10−7 | 4.4 × 10−6 | 3.4 (2.2–5.3) | ||||
rs320035 | 1 (49089197) | A/G (G) | GWAS | 48/354 | 0.48 | 3.5 × 10−6 | 1.3 × 10−4 | 2.4 (1.5–3.8) | AGBL4 |
Rep | 27/216 | 0.50 | 4.2 × 10−3 | 1.2 × 10−2 | 2.2 (1.9–3.9) | ||||
Comb | 75/570 | 0.49 | 8.2 × 10−7 | 5.1 × 10−6 | 2.3 (1.6–3.3) | ||||
rs10946739 | 6 (24993127) | A/G (A) | GWAS | 48/354 | 0.19 | 9.6 × 10−6 | 4.1 × 10−6 | 3.4 (2.0–5.6) | FAM65B |
Rep | 25/209 | 0.18 | 1.1 × 10−1 | 1.8 × 10−1 | 1.7 (0.8–3.6) | ||||
Comb | 73/563 | 0.19 | 4.7 × 10−6 | 5.1 × 10−6 | 2.7 (1.8–4.1) | ||||
rs393994 | 1 (49108745) | T/C (C) | GWAS | 48/354 | 0.48 | 6.1 × 10−6 | 1.7 × 10−4 | 2.4 (1.5–3.7) | AGBL4 |
Rep | 27/216 | 0.50 | 7.9 × 10−3 | 1.4 × 10−2 | 2.1 (1.2–4.0) | ||||
Comb | 75/570 | 0.49 | 1.9 × 10−6 | 7.6 × 10−6 | 2.3 (1.6–3.3) | ||||
rs320003 | 1 (49126778) | A/G (A) | GWAS | 48/354 | 0.48 | 1.7 × 10−5 | 2.3 × 10−4 | 2.3 (1.5–3.7) | AGBL4 |
Rep | 23/208 | 0.50 | 1.9 × 10−2 | 1.2 × 10−2 | 2.3 (1.2–4.5) | ||||
Comb | 71/562 | 0.49 | 4.6 × 10−6 | 8.3 × 10−6 | 2.3 (1.6–3.4) | ||||
rs319952 | 1 (49113622) | A/G (G) | GWAS | 48/354 | 0.48 | 1.1 × 10−5 | 2.8 × 10−4 | 2.3 (1.5–3.6) | AGBL4 |
Rep | 26/216 | 0.50 | 1.2 × 10−2 | 1.0 × 10−2 | 2.3 (1.2–4.4) | ||||
Comb | 74/570 | 0.49 | 2.5 × 10−6 | 8.5 × 10−6 | 2.3 (1.6–3.3) | ||||
rs7958375 | 1 (2 111640017) | A/G (A) | GWAS | 48/354 | 0.02 | 8.8 × 10−5 | 1.2 × 10−5 | 11.3 (3.8–33.5) | CUX2 |
Rep | 27/216 | 0.02 | 1.0 × 10+0 | 7.4 × 10−1 | 1.5 (0.2–13.1) | ||||
Comb | 75/570 | 0.02 | 1.7 × 10−4 | 4.6 × 10−5 | 7.6 (2.9–20.0) |