Table 1.
Locations and allele frequencies of the SNPs most highly associated with the VL phenotype. The number of VL affected individuals for each genotype is shown to provide insight into the possible effect of each allele. p-Values provided are: pun for uncorrected, pes for empirical simulation corrected, pcorr for modified Bonferroni correction (i.e. uncorrected p-value multiplied by 961 LD blocks). The overall threshold for significance taking account of the number of LD blocks is p = 5.2e−05 (i.e. p = 0.05/961 LD blocks) for an α = 0.05.
| Associated SNP | Position relative to nearest genes | Population allele frequencies | Genotype frequencies | Total (affected) per genotype | p-Values |
|---|---|---|---|---|---|
| rs1470217 | 115 kb downstream of TMEM215 | A = 0.678 | GG = 0.13 | GG = 107 (13) | pun = 5.9e−05 |
| Chr 9p21.1 | 69 kb downstream of APTX | G = 0.322 | AG = 0.45 | AG = 299 (78) | pes = 0.089 |
| Intergenic | AA = 0.42 | AA = 259 (48) | pcorr = 0.057 | ||
| rs8107014 | LTBP4 | C = 0.539 | CC = 0.34 | CC = 254 (48) | pun = 1.4e−05 |
| Chr 19q13.2 | Intronic | T = 0.461 | CT = 0.5 | CT = 331 (63) | pes = 0.022 |
| TT = 0.16 | TT = 80 (28) | pcorr = 0.013 |