Association of LPL HTs with lipid concentration
Two blocks, including SNPs located in the LPL gene, were identified (Supplementary Fig. 2), and the association of HT with lipid profiles for the two blocks was examined. The analysis using combined data from the two stages showed that block 2, which includes SNPs located in the LPL gene, including the 3' flanking region, was the region most strongly associated with lipid concentrations (Table 3). HT3 in block 2 was strongly associated with increased HDLC levels (p = 2.86 × 10-22; 2.25-mg/dL increase per HT3) and reduced TG levels (p = 9.09 × 10-15; 13.7-mg/dL decrease per HT3), whereas HT1 was strongly associated with reduced HDLC levels (p = 1.1 × 10-14; 1.2-mg/dL decrease per HT1) and higher TG levels (p = 3.05 × 10-12; 8.6-mg/dL increase per HT1). There was no significant association between HT and either LDLC or TCHL.
The analysis using imputed data also showed a strong association between HTs and lipid levels in the 2 blocks, including LPL SNPs (Supplementary Table 3). HT1 in block 2 was significantly associated with a reduced HDLC level (p = 4.2 × 10-15; 1.3-mg/dL decrease per HT1) and an increased level of TG (p = 1.9 × 10-8; 8-mg/dL increase per HT1), whereas HT3 was significantly associated with increased HDLC (p = 7.8 × 10-16; 2-mg/dL increase per HT3) and LDLC levels (p = 5.1 × 10-3; 2.3-mg/dL increases per HT3) and decreased TG levels (p = 5.6 × 10-13; 15.1-mg/dL decrease per HT3).