Table 2.

Association results for the two replicated Buruli ulcer GWAS signals.

					Discovery	Replication	Combined sample
SNP	Chr	Positiona	Gene	M/mb	P valuec	P valuec,d	MAF Controls	MAF Cases	P valuec	Effect sizee
rs9814705*	3	145680345	ENSG00000240095.1	T/C	1.67 × 10−4	6.51 × 10−4	0.10	0.16	2.85 × 10−7	1.80 (1.43–2.27)
rs76647377	6	985196	LINC01622	G/A	1.78 × 10−6	3.26 × 10−3	0.05	0.02	9.85 × 10−8	0.41 (0.28–0.60)

^aGRCh37.p13.

^bAllele m is the minor allele and M is the major allele in the combined cohort.

^cDiscovery, replication and combined P values obtained when the logistic model (Buruli ulcer per se phenotype) is considered for rs9814705, and when the Cox model (taking age at onset into account) is considered for rs76647377. When considering mixed-models in the discovery sample, i.e. GEMMA for rs9814705 and coxme for rs76647377, discovery P values are 2.13 × 10⁻⁴ and 2.06 × 10⁻⁶, respectively.

^dOne-tailed test.

^eEffect size corresponds to odds ratios (95% confidence interval) when the logistic model (Buruli ulcer per se phenotype) is considered (rs9814705), and hazard ratios (95% confidence interval) when the Cox model (taking age at onset into account) is considered (rs76647377). Effect size is assessed under an additive model, using the minor allele as the reference.

*rs9814705 was resequenced in the discovery sample.