Table 3a-d.

Haplotypes of variation at five loci influencing innate immunity in a Black South African cohort, n=138.

Table 3a. Haplotypes in IFIH1 on chromosome 2 (encodes MDA5).
SNP	rs1990760	rs3747517	rs10930046	rs984971
reference allele	C	C	T	G
minor allele	T	T	C *	A
mutation type	missense	missense	missense	intron	frequency
ht1	.	.	C	.	0.480
ht2	.	T	.	.	0.391
ht3	.	.	C	A	0.057
ht4	T	.	.	A	0.050
ht5	T	.	.	.	0.012
ht6	.	T	.	A	0.010
Table 3b. Haplotypes in DDX58 on chromosome 9 (encodes RIG-1).
SNP	rs55789327	rs669260	rs10813831
reference allele	G	T	G
minor allele	A	C	A
mutation type	missense	intron	missense	frequency
ht1	.	.	.	0.463
ht2	.	C	.	0.234
ht3	.	.	A	0.220
ht4	A	.	.	0.083
Table 3c. Haplotypes in TLR3 on chromosome 4.
SNP	rs5743305	rs13126816	rs3775296	rs5743312	rs3775292	rs10025405
reference allele	T	G	C	C	G	A
minor allele	A	A	A	T	C	G
mutation type	5’ TF binding site	intron	splice region	intron	non coding exon	3’ UTR	frequency
ht1	.	.	.	.	.	.	0.417
ht2	A	.	.	.	.	.	0.179
ht3	.	.	.	.	.	G	0.116
ht4	.	.	.	.	C	.	0.068
ht5	.	.	A	T	.	G	0.056
ht6	.	A	.	.	.	.	0.032
ht7	.	.	A	T	.	.	0.029
ht8	.	.	A	.	.	.	0.028
ht9	A	.	.	.	.	G	0.025
ht10	A	A	.	.	.	.	0.020
Table 3d. Haplotypes of SNPs in TLR7 and TLR8 on chromosome X.
Gene	TLR7	TLR7	TLR7	TLR7	TLR7	TLR8
SNP	rs179008	rs864058	rs3853839	rs179007	rs5935438	rs2159377
reference allele	A	G	C	A	G	C
minor allele	T	A	G	G	C	T
mutation type	missense	synonymous	3’ UTR	intergenic	TF binding site	synonymous	frequency
ht1	.	A	.	G	.	.	0.205
ht2	.	.	.	.	C	.	0.188
ht3	.	.	.	.	.	.	0.175
ht4	.	.	.	.	.	T	0.064
ht5	.	.	G	.	.	.	0.063
ht6	.	A	.	.	C	.	0.062
ht7	.	A	.	.	.	.	0.057
ht8	T	.	.	.	.	.	0.034
ht9	.	.	.	G	.	.	0.029
ht10	.	A	.	.	C	T	0.026
ht11	.	.	G	.	.	T	0.017
ht12	T	.	.	.	C	.	0.013
ht13	T	A	.	.	.	.	0.011
ht14	.	A	.	G	C	.	0.012
ht15	T	.	.	G	.	.	0.010

^*C is the minor allele in most populations but MAF in SA was >0.5. T allele is considered to be wild type.

Dots indicate identity to reference allele.