MixMAP results in GLGC for IBC array loci with evidence for single SNP LDL-C association.

For the 31827 SNPs in 2960 genes interrogated in Global Lipids Genetic Consortium (GLGC) summary data [1], MixMAP detects 36 genes in 21 of 26 loci detected by single SNP analysis in GLGC. Coverage of genes detected by both approaches is higher, while the median p-value is generally lower, than that of genes detected by single SNP analysis alone. ‡Genes were assigned to a locus identified in the GLGC [1] if SNPs in that gene were within 500 Kb of or had linkage disequilibrium (LD) with the top SNP at a GLGC genome wide significant locus. †Genes designated at genome wide significant locus in GLGC were not directly interrogated in IBC array data; indicates corresponding gene detected and – indicates corresponding gene not detected; genome wide significant threshold (); Bonferroni correction based on the number of genes (); Gene is significant based on Single SNP approach in [1] (Table 1) but significant SNP is not included in IBC array under study; This gene is significant based on single SNP approach for TC and HDL in GLGC [1] (Table 1) and conditionally associated with LDL (Table 6 Supp); Limited LD () detected; however, assigned to same locus due to physical proximity (Kb) and/or multiple candidate genes in the region. These may represent signal for LDL-C independent of the established GLGC locus.