Table 5 Signals of human association in the MeninGene cohort

From: Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

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

  1. 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
  2. MAF minor allele frequency, OR odds ratio, SNP single-nucleotide polymorphism, TSS transcription start site
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