Genetic variants of TLR4, including the novel variant, rs5030719, and related genes are associated with susceptibility to clinical malaria in African children

Table 3 Genes and their haplotypes that are statistically associated with the incidence of clinical malaria via haplotype trend regression (HTR) analysis

Gene	Maternal/child	Haplotype	f-statistic	p-value	rs_value	Chromosome	Position (hg38)
ABO	Child	CAA	4.984505	0.028	rs8176747; rs8176746; rs8176743	9	133255928; 133255935; 133256028
ABO	Child	GCG	4.984505	0.028	rs8176747; rs8176746; rs8176743	9	133255928; 133255935; 133256028
IFNGR1	Maternal	AT(TT)	2.653187	0.073	rs7749390; rs2234711; rs41401746	6	137219233; 137219383; 137219797–137219798
IFNGR1	Maternal	GC(TT)	2.653187	0.073	rs7749390; rs2234711; rs41401746	6	137219233; 137219383; 137219797–137219798
IL13	Child	GCACT	1.090957	0.373	rs2069739; rs1800925; rs2069743; rs2066960; rs20541	5	132656916; 132657117; 132657583; 132658743; 132660272
IL13	Child	GTGCT	1.090957	0.373	rs2069739; rs1800925; rs2069743; rs2066960; rs20541	5	132656916; 132657117; 132657583; 132658743; 132660272
IL6	Maternal	GCT	4.347798	0.018	rs1800796; rs1800795; rs2069830	7	22726627; 22727026; 22727518
TLR4	Maternal	GT	3.42998	0.027	rs4986790; rs5030719	9	117713024; 117713658
TLR4	Child	AT	3.734751	0.021	rs4986790; rs5030719	9	117713024; 117713658

The ‘maternal/child’ column defines if the gene and haplotype was identified in the maternal or children genomes, the ‘haplotype’ column lists the alleles found in the haplotype in sequence of increasing genomic position, further defined in the columns ‘rs_value’ (as defined in the NCBI dbSNP repository), ‘chromosome’, and ‘position’ (as annotated in human whole genome build hg38). The ‘f-statistic’ and ‘p-value’ columns respectively detail the Fisher-statistic for goodness-of-fit of the haplotype to the tested model and haplotype trend regression (HTR) p-value for association of the haplotype with primary cases of clinical malaria. The two haplotypes for IFNGR1 involve rs41401746, which represents a dinucleotide polymorphism, and is represented here in brackets (TT). Further description is given in Additional file 1: Table S1

ISSN: 1475-2875