Table 2. Strongest suggestive GWA loci (p < 5 × 10−6) from RSV bronchiolitis GWAS and SNPs selected for replication genotyping from each locus.
| Suggestive RSV GWA locus╤ | Selected SNP information | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | RangeЖ | Span (kb) | SNPs | Lowest p | SNP name | LocationЖ | Genes** | A1 | MAF |
OR‡ (95% CI) | p | |
| Cases | Controls | |||||||||||
| 1 | 153512691..153996110 | 483 | 6 | 5.2 × 10−7 | rs75940909 | 153932075 | SLC39A1 | A | 0.063 | 0.011 | 5.58 (2.69–11.93) | 9.2 × 10−6 |
| 1 | 154011426..154260767 | 249 | 4 | 1.1 × 10−6 | rs186841738 | 154187935 | C1orf43 | A | 0.062 | 0.009 | 6.73 (3.02–15.01) | 3.1 × 10−6 |
| 2 | 36592600..36617435 | 24 | 2 | 2.4 × 10−6 | rs112913823 | 36617435 | CRIM1 | G | 0.086 | 0.025 | 4.38 (2.37–8.09) | 2.4 × 10−6 |
| 3 | 185675973..185677613 | 1 | 9 | 4.9 × 10−6 | rs6444089 | 185676350 | TRA2B, ETV5 | G | 0.277 | 0.410 | 0.48 (0.34–0.66) | 8.7 × 10−6 |
| 3 | 185675973..185677613 | 1 | 9 | 4.9 × 10−6 | rs55675198 | 185677613 | TRA2B, ETV5 | G | 0.252 | 0.391 | 0.46 (0.33–0.64) | 6.2 × 10−6 |
| 4 | 32653789..32869901 | 216 | 52 | 4.7 × 10−6 | rs4547837 | 32688632 | LOC107986223, LOC101927363 | T | 0.054 | 0.010 | 6.55 (2.93–14.65) | 4.7 × 10−6 |
| 7 | 46319511..46524796† | 205 | 9 | 6.9 × 10−7 | rs62452699 | 46492326 | LOC105375265, LOC105375266 | T | 0.149 | 0.061 | 3.37 (2.09–5.45) | 6.9 × 10−7 |
| 7 | 148765688..148959272 | 193 | 21 | 5.5 × 10−7 | rs139743624 | 148870713 | ZNF398 | A | 0.051 | 0.010 | 6.51 (2.86–14.86) | 8.5 × 10−6 |
| 10 | 50452677..50460878† | 8 | 10 | 3.1 × 10−7 | rs17009617 | 50453933 | VSTM4, C10orf71 | A | 0.111 | 0.032 | 4.16 (2.41–7.19) | 3.1 × 10−7 |
| 10 | 50454331..50553085† | 98 | 50 | 1.2 × 10−7 | rs76728164 | 50465201 | C10orf71, DRGX | T | 0.106 | 0.033 | 3.46 (2.05–5.85) | 3.6 × 10−6 |
| 10 | 50454331..50553085† | 98 | 50 | 1.2 × 10−7 | rs1001338 | 50498449 | C10orf71, DRGX | G | 0.112 | 0.031 | 3.95 (2.33–6.69) | 3.6 × 10−7 |
| 15 | 39354517..39515134 | 160 | 46 | 6.5 × 10−7 | rs75360543 | 39505815 | LOC105370777 | G | 0.104 | 0.034 | 4.10 (2.35–7.14) | 6.5 × 10−7 |
╤Each suggestive GWA locus comprises several SNPs in LD (r2 > 0.5, p < 0.01). Loci were formed with default options of LD-based result clumping (PLINK 1.9). We selected one variant for replication genotyping from each locus. Signals in sporadic imputed variants (not shown) were considered unreliable and not chosen for replication genotyping.
ЖRange and location refer to human genome build 37 (GRCh37/hg19) base pair positions.
**Corresponding locus shown for variants within genes; two nearest genes shown for intergenic SNPs.
‡OR for A1 allele under additive model in logistic regression, with sex and three principal components as covariates.
†Suggestive GWA loci shared between GWAS and RSV GWAS (of loci with p < 5 × 10−6).
GWA, genome-wide association; RSV, respiratory syncytial virus; SNP, single nucleotide polymorphism; Chr, chromosome; MAF, minor allele frequency; OR, odds ratio; CI, confidence interval; LD, linkage disequilibrium.