TABLE 5.

Results from Fisher’s exact test for association of individual variants in the classical class I genes HLA-A, -B, and –C obtained by variant calling of the HTS data.

CHR	Position	Ref	Alt	Cases	Tolerants	P	OR	Gene	Exon/Intron	Comment
6	31237779	C	T	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Exon 5	Co-occured with C*04:01:01
6	31238027	C	A	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Exon 4
6	31238267	C	T	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Intron 3
6	31238538	G	C	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Intron 3
6	31239082	G	C	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Exon 3
6	31239501	G	T	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Exon 2
6	31239607	G	A	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Exon 2
6	31239742	G	C	1 (2%)	12 (16%)	0.0063	0.087	HLA-C	Intron 1
6	31239652	G	A	3 (5%)	15 (20%)	0.011	0.21	HLA-C	Intron 1
6	31239660	G	T	3 (5%)	15 (20%)	0.011	0.21	HLA-C	Intron 1
6	31237987	C	T	2 (3%)	13 (17%)	0.012	0.16	HLA-C	Exon 4
6	31239057	C	T	5 (8%)	18 (24%)	0.020	0.28	HLA-C	Exon 3
6	31238928	TCA	T	4 (6%)	0 (0%)	0.039	NA	HLA-C	Exon 3	Co-occured with C*07:04:01

Only variants with p < 0.05 are shown and sorted according to p-value. Number of alleles and allele frequency (%) of the alternate allele (Alt) of cases and tolerant controls are indicated in the columns “Cases” and “Tolerants” respectively. Blocks of variants which are present in the same samples are highlighted in one block of the same shade of gray. If a shown variant co-occurred with a candidate HLA allele in the discovery subset, i.e., 100% of Alt allele carriers also carried the respective candidate allele, it is indicated in the column “Comment.” Genomic positions are based on hg19.