Swine inflammation and necrosis syndrome (SINS) is a widespread disease in pigs, causing pain, suffering, and damage. Inflammation is documented at different levels based on clinical signs, histopathology, clinical chemistry, metabolomics and transcriptomics. The influence of sow and boar, as well as a heritability of around 0.3, suggest a genetic component to the disease. The aim of the present study was to identify functional single nucleotide polymorphisms (SNPs) in the vicinity of gene markers previously mapped using GWAS. DNA samples were available from 234 already phenotyped piglets. These animals were re-sequenced with additional prior enrichment. The nine selected chromosomal regions cover a total length of 22 Mbp. The genome-wide association study (GWAS) revealed two series with a total of 15 significant missense polymorphisms on chromosomes 11, 14, and 15. The homozygous genotypes of the most discriminating SNPs in series 1 resulted in SINS scores of 3.5 and 17.9, respectively. Despite the partial linkage of the SNPs, interesting candidate genes were defined. The results allow a significant narrowing of the possible candidate genes for understanding the pathogenesis of SINS and for future use in selection breeding to overcome the syndrome. Further studies should be carried out on larger animal populations.