Table 2.
Top SNPs in the combined analysis of the GWAS and the replication study
| SNP | Chr (loci) | Alleles (RA) | Study | Cases/controls | MAF | P_min | P_adj | OR (95 % 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) |
Chr (loci) Chromosome, and chromosomal loci based on NCBI built 37, CI Confidence Interval, Comb Combined analysis using inverse variance method, GWAS Genome wide association study, MAF Minor allele frequency, OR Odds ratio, P_adj Logistic P-value after adjustment for sex, HIV status, CD4 count and HIV viral load; P_min Minimum P-value among allelic, dominant and recessive models of Fisher’s exact test, and P-value of inverse variance combined analysis; RA Risk allele, Rep Replication study, SNP Single nucleotide polymorphism