Table 5.
Signals of human association in the MeninGene cohort
| Phenotype | Position (SNP) | Marker | Effect allele | MAF | OR | p-value | Annotation |
|---|---|---|---|---|---|---|---|
| Susceptibility (pneumococcal meningitis only) | chr6:117624549 | (rs210967) | G | 0.46 | 0.77 | 8.8 × 10–7 | ROS1 intronic |
| chr18:48403560 | (rs2850542) | T | 0.43 | 0.65 | 7.6 × 10–8 | ME2 promoter (2 kb upstream of TSS) | |
| chr22:47506160 | (rs13057743) | G | 0.33 | 0.74 | 5.5 × 10–7 | TBC1D22A intronic | |
| Severity (any species) | chr1:64680775 | (rs12081070) | A | 0.43 | 1.62 | 2.0 × 10–8 | UBE2U (fifth intron)/ROR1 |
| chr4:182823804 | (rs2309554) | A | 0.33 | 1.58 | 4.1 × 10–7 | AC108142.1 intron | |
| chr9:37382231 | (rs72739603) | A | 0.07 | 2.36 | 6.7 × 10–7 | ZCCHC7/GRHPR |
We report the lead SNP at each putatively associated locus with MAF > 5% and p < 1 × 10–6, and nearby annotated genes. p < 5 × 10–8 is the genome-wide significance threshold—only rs12081070 exceeds this. The suggestive signal in all meningitis cases at rs3870369 was also present when restricted to pneumococcal cases, albeit with a lower p value of 3.9 × 10–7
MAF minor allele frequency, OR odds ratio, SNP single-nucleotide polymorphism, TSS transcription start site