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Table 2 Genes significantly associated with lipid traits in at least one test on the ESP

From: PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection

Trait Gene Pval PSCAN-M Pval PSCAN-V Pval SCAN1D-M Pval SCAN1D-V Pval Burden Pval SKAT #SNP Total #Signal SNP in (PSCAN-M,-V), (SCAN1D-M,-V), SV
HDL CD36 1.2×10−6 2.6×10−7 9.0×10−3 3.9×10−7 2.7×10−4 1.1×10−7 70 (2,2), (0,48), 1
  CETP 6.9×10−7 2.4×10−9 7.0×10−9 1.1×10−9 4.9×10−4 9.1×10−8 35 (3,4), (2,3), 1
  NCK1 3.6×10−1 6.5×10−6 4.0×10−1 2.4×10−6 2.5×10−1 6.2×10−6 12 (0,12), (0,7), 1
  PCSK7 1.8×10−6 1.8×10−6 2.6×10−6 1.7×10−6 1.4×10−1 2.4×10−3 28 (1,1), (1,1), 1
TRIG APOC3 1.5×10−5 1.2×10−5 3.6×10−8 1.1×10−5 3.9×10−6 3.2×10−6 7 (7,7), (4,4), 2
  ARSI 1.4×10−1 1.5×10−5 6.1×10−1 1.9×10−1 7.3×10−2 4.0×10−2 28 (0,9), (0,0), 0
  CYP2C9 4.4×10−6 4.0×10−2 5.1×10−5 4.6×10−2 6.4×10−7 1.6×10−2 33 (30,0), (16,0), 0
  NFATC1 3.3×10−2 1.4×10−7 5.6×10−2 1.5×10−6 1.7×10−1 5.9×10−2 35 (0,6), (0,7), 0
  PGM1 2.8×10−4 9.9×10−6 2.3×10−1 2.9×10−1 9.9×10−1 7.2×10−2 27 (3,3), (0,0), 1
  1. The association test p-values and the numbers of identified signal variants at α=0.05/5=0.01 level are presented