Table 4. Top associated genes with heterogenous variation across multiple individuals.
|
Allele frequency in each population |
|||||||
|---|---|---|---|---|---|---|---|
| Gene | Phevor score | Phevor P-value | SNP; locus | Variant; AA change | Asthma risk group, % (n=28) | Other UT suicides, % (n=432) (gene P-value) | CEU/GBR, % (n=183) (gene P-value) |
| TLR3 | 3.16 | 0.0007 | rs112077022; chr4:187003678 | G/A; D/N | 1.80 | 0 (0.0314) | 0 (0.0442) |
| rs199768900; chr4:187005912 | G/A; R/Q | 1.80 | 0.12 (0.0314) | 0 (0.0442) | |||
| ALAS2 | 2.98 | 0.0011 | rs201799139; chrX:55035659 | G/A; S/F | 2.80 | 0 (0.00838) | 0.36 (0.0442) |
| rs201062903; chrX:55039960 | G/A; P/L | 2.80 | 0 (0.00838) | 0 (0.0442) | |||
| rs145704441; chrX:55035701 | C/T; R/H | 2.80 | 0 (0.00838) | 0 (0.0442) | |||
| FAM184B | 2.6 | 0.0025 | rs61742285; chr4:17640880 | C/G; E/Q | 5.40 | 3.4 (0.0456) | 0.83 (0.00094) |
| rs61746992; chr4:17710586 | C/G; D/H | 1.80 | 0.23 (0.0456) | 0 (0.00094) | |||
| rs61746445; chr4:17711210 | G/A; R/W | 1.80 | 0.46 (0.0456) | 0 (0.00094) | |||
| rs191859569; chr4:17654594 | G/A; R/C | 1.80 | 0 (0.0456) | 0.35 (0.00094) | |||
| rs151185488; chr4:17707448 | C/G; G/A | 1.80 | 0.81 (0.0456) | 0 (0.00094) | |||
| NCAM2 | 2.43 | 0.0037 | rs200376885; chr21:22652906 | C/A; Q/K | 1.80 | 0.23 (0.0428) | 0 (0.0357) |
| rs200645709; chr21:22658669 | A/G; S/G | 1.80 | 0 (0.0428) | 0 (0.0357) | |||
| SLC22A11 | 2.39 | 0.0041 | rs35008345; chr11:64323613 | C/T; R/* | 1.80 | 0.12 (0.0314) | 0 (0.03) |
| rs147522958; chr11:64331790 | G/A; E/K | 1.80 | 0.23 (0.0314) | 0 (0.03) | |||
| KRTAP27-1 | 2.31 | 0.0049 | rs144648271; chr21:31709731 | G/A; Q/* | 3.60 | 0.12 (0.00742) | 0 (0.0266) |
| rs139988725; chr21:31709679 | T/A; E/V | 1.80 | 0.12 (0.00742) | 0.55 (0.0266) | |||
| PCDHGB5 | 2.28 | 0.0053 | rs140768844; chr5:140768844 | C/T; P/S | 1.80 | 0.23 (0.0471) | 0 (0.0456) |
| rs199849689; chr5:140790021 | C/T; S/F | 1.80 | 0.12 (0.0471) | 0.43 (0.0456) | |||
| rs199531162; chr5:140789304 | G/C; G/A | 1.80 | 0 (0.0471) | 0 (0.0456) | |||
| CDK6 | 2.18 | 0.0065 | rs14049009; chr7:92244486 | T/A; S/C | 1.80 | 0.35 (0.0485) | 0 (0.0227) |
| rs35654944; chr7:92404051 | C/T; D/N | 1.80 | 0.23 (0.0485) | 0.55 (0.0227) | |||
| VTN | 2.15 | 0.007 | rs140531078; chr17:26695904 | T/C; Y/C | 1.90 | 0 (0.00619) | 0 (0.0187) |
| rs113837940; chr17:26694852 | G/A; S/F | 1.80 | 0 (0.00619) | 0 (0.0187) | |||
| DAB2IP | 2.13 | 0.0074 | rs117152313; chr9:124544697 | C/T; R/C | 1.90 | 0.23 (0.0485) | 0 (0.018) |
| rs143836788; chr9:124536561 | A/G; N/S | 1.90 | 0 (0.00619) | 0 (0.018) | |||
| rs141706892; chr9:124526082 | G/A; A/T | 1.80 | 0.12 (0.0442) | 0 (0.018) | |||
| R3HDM1 | 2.05 | 0.0088 | rs34088964; chr2:136396212 | A/C; I/L | 3.60 | 0.35 (0.0399) | 0 (0.00213) |
| rs151233134; chr2:136418898 | C/T; P/L | 1.80 | 0.12 (0.0399) | 0 (0.00213) | |||
| rs2305165; chr2:136409574 | A/C; Q/P | 10.70 | 8.5 (0.0399) | 6.83 (0.00213) | |||
| PLEKHG3 | 2.01 | 0.0097 | rs141719183; chr14:65205490 | A/G; R/G | 3.60 | 0.23 (0.0471) | 0.27 (0.0286) |
| rs142732386; chr14:65198849 | C/T; H/Y | 1.80 | 0.12 (0.0471) | 0 (0.0286) | |||
Abbreviations: *, stop codon/nonsense; ALAS2, delta aminolevulinate synthase 2; CDK6, cyclin-dependent kinase 6; CEU, western European ancestry; DAB2IP, DAB2 interacting protein; FAM184B, family with sequence similarity 184, member B; GBR, British in England and Scotland; KRTAP27-1, keratin associated protein 27-1; NCAM2, neural cell adhesion molecule 2; PCDHGB5, protocadherin gamma subfamily B, 5; Phevor, phenotype driven variant ontological re-ranking tool; PLEKHG3, pleckstrin homology domain containing, family G, member 3; R3HDM1, R3H domain containing 1; SLC22A11, solute carrier family 22, member 11; SNP, single-nucleotide polymorphism; TLR3, Toll-like receptor 3; UT, Utah; VTN, vitronectin.
All pVAAST (pedigree extension of the Variant Annotation, Analysis and Search Tool) P-values were computed using 109 permutations. Frequencies between each group were calculated using chromosome counts, accounting for subjects with no calls. No homozygotes were observed for these variants.