Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

Table 4 Number and annotation of ASE-SNPs affecting MHC genes

	SLA-1	SLA-2	SLA-3	SLA-5	SLA-7	SLA-11	SLA-DRA	SLA-DRB1	SLA-DOA	SLA-DQB1/2
3’UTR variant	13	15				6	1			3
5’UTR variant						1
Intron variant	17	5	13		2			2
Misssense variant	28	2			1	7		14
Non-coding transcript exon variant	2		61	12
Splice region variant	12	1	1
Synonymous variant						3		6	1
Downstream gene variant		4	12		3	3		6
Intergenic variant
Total^a	72	27	84	12	3	20	1	28	1	3

^a Total of ASE-SNPs per gene identified in the 38 pigs included in the analysis. The total numbers do not correspond to the sum of annotated SNPs because a few SNPs were annotated differently depending on the transcript they overlapped

ISSN: 1471-2164