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Table 3 The hub SNPs/genes identified in the top-ranked 1000 SNP pairs

From: iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

Hub SNPs from analyses of complete SNP set
Disease Hub SNPs (Genomic position) # Interacting SNPs
BD rs1553460 (Chr4:17804959) 1000
CAD rs3785579 (Chr17:62472963) 1000
CD rs1553460 (Chr4:17804959) 978
  rs4471699 (Chr16:30227808) 22
HT rs10843660 (Chr12:30259724) 999
RA rs3785579 (Chr17:62472963) 1000
T1D rs9273363 (Chr6:32734250) 1000
T2D rs7077039 (Chr10:114779067) 833
  rs10787472 (Chr10:114771287) 54
  rs11196208 (Chr10:114801306) 39
  rs11196205 (Chr10:114797037) 30
  rs10885409 (Chr10:114798062) 22
  rs4074720 (Chr10:114738487) 17
Hub genes from gene-only SNP analyses
Disease Hub genes # Interacting genes
BD CENPN: centromere protein N 653
CAD CACNG1: calcium channel, voltage-dependent, gamma subunit 1 709
CD ATG16L1: ATG16 autophagy related 16-like 1 (S. cerevisiae)*** 256
  IL23R: interleukin 23 receptor *** 20
HT tcag7.23: similar to ribosomal protein L18; 60S ribosomal protein L18 170
  BCAT1: branched chain aminotransferase 1, cytosolic *** 57
  SAMD4A: sterile alpha motif domain containing 4A * 27
  GAB1: GRB2-associated binding protein 1 * 25
  RHOJ: ras homolog gene family, member J 20
  LYPD5: LY6/PLAUR domain containing 5 * 12
RA CACNG1: calcium channel, voltage-dependent, gamma subunit 1 676
T1D HLA-DQB1: major histocompatibility complex, class II, DQ beta 1** 686
T2D TCF7L2: transcription factor 7-like 2 (T-cell specific, HMG-box)*** 481
  1. * Genes associated with disease SNPs that were previously reported in WTCCC original paper
  2. ** Genes previously reported to be disease-associated in HuGE Navigator database
  3. *** Genes previously reported to be disease-associated in both WTCCC paper and HuGE Navigator database