Table 2.

Statistically Significant SNPs Identified in Extrapulmonary Tuberculosis Cases vs. PPD + Controls

SNP	Rank	P-value	MAF in ETB	MAF in PPD +	Odds Ratio	Chromosome	Gene	Closest Gene	Distance to Gene
rs4893980	1	0.0007	0.1087	0.4902	0.1268	2	PDE11A	---	---
rs10487416	2	0.0007	0.25	0.0566	5.556	7	unknown	unknown	unknown
rs10488286	3	0.0009	0.2381	0.02727	11.15	7	KCND2	---	---
rs2026414	4	0.0009	0.5208	0.2589	3.111	10	PCDH15	---	---

Empirical P - value cutoff from permutation testing = 0.0009

The p - value reported is the raw value.

MAF = Minor Allele Frequency

ETB = Extrapulmonary tuberculosis

PPD + = Purified protein derivative positive