Table 1.

Top candidate gene SNP associations for VL and DTH phenotypes.

SNP	Trait1	Ref. 2 Allele	Freq. 2	LOD	Pnominal3	Pcorrected3	Causal Allele	Gene	Location4
rs6785358	VLvsALL	A	0.836	3.25	5.7E-04	0.027	G	TGFBR2	upstream
rs6770038	VLvsALL	C	0.72	3.06	8.7E-04	0.042	T	TGFBR2	intron
rs10800309	VLvsALL	G	0.699	2.77	0.0017	0.082	G	FCGR2A	upstream
rs2306191	VLvsALL	C	0.898	2.62	0.0024	0.115	G	IL27RA	intron
rs2279015	VLvsALL	T	0.601	2.27	0.0054	0.259	T	SLC11A1	intron
rs1882434	VLvsALL	C	0.649	2.07	0.0085	0.408	T	COL4A4	intron
rs6785358	VLvsDTH	A	0.836	1.87	0.013	0.642	G	TGFBR2	upstream
rs6770038	VLvsDTH	C	0.72	3.08	8.3E-04	0.039	T	TGFBR2	intron
rs10800309	VLvsDTH	G	0.699	2.53	0.003	0.144	G	FCGR2A	upstream
rs2306191	VLvsDTH	C	0.898	1.58	0.026	1.248	G	IL27RA	intron
rs2279015	VLvsDTH	T	0.601	2.16	0.007	0.336	T	SLC11A1	intron
rs1882434	VLvsDTH	C	0.649	2.42	0.0038	0.182	T	COL4A4	intron
rs10800309	DTH+vsDTH−	G	0.699	5.07	8.4E-06	3.9E-04	A	FCGR2A	upstream
rs7238442	DTH+vsDTH−	C	0.559	2.94	0.001	0.051	T	SMAD7	intron
rs4586	DTH+vsDTH−	C	0.537	2.49	0.003	0.147	T	CCL2	intron
rs2337106	DTH+vsDTH−	C	0.589	2.18	0.007	0.304	G	SMAD7	intron
rs2239347	DTH+vsDTH−	G	0.519	2.05	0.009	0.414	G	IL4R	intron

¹Phenotypes were analysed as qualitative traits (VL_vsALL = VL present versus all DTH+ and known DTH− individuals; VL_vsDTH = VL present versus DTH+, DTH− set to unknown; DTH⁺_vsDTH⁻ = DTH positive ≥5mm induration versus DTH negative <5mm induration, VL set to unknown).

²Reference Allele, and Frequency of Reference Allele.

³P-values provided are: p_nominal for uncorrected; p_correctedfor modified Bonferroni correction (i.e. uncorrected p-value multiplied by 48 LD blocks). The overall threshold for significance taking account of the number of LD blocks is p=0.001 (i.e. p=0.05/46 LD blocks) for an α=0.05.

⁴The location of the SNP is given relative to the candidate gene.