We identified a subset of associations potentially involved in the immunogenetic regulation of lipid metabolism including rs10951261—ApoB (βME/CFS adjusted = −0.02, βHC = 0.02, I2p = 1.60 × 10−6), rs4752983—concentration of large HDL particles (L-HDL-P) (βME/CFS adjusted = 0.02, βHC = −0.04, I2p = 3.35 × 10−6), and rs10432735—cholesteryl esters in large LDL (L-LDL-CE) (βME/CFS = 0.03, βHC = −0.05, I2p = 3.59 × 10−6), with the three variants mapping to ADAP1, NR1H3, and CD40, respectively. Here, NR1H3 is linked to myalgic encephalomeyelitis/chronic fatigue syndrome.