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Table 1 Bonferroni significant cis-trans interactions in the liver, pre-frontal cortex and the cerebellum

From: Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression

Tissue Cis-SNP Cis position Trans SNP Trans position Transcript Interaction p-value Effect size
Liver rs3129045 6:29652576 rs7761068 6:31333939 HLA-G 9.35 × 10−7 54.67
  rs2747442 6:29653186 rs7761068 6:31333939 HLA-G 2.22 × 10−5 47.63
  rs2747436 6:29651935 rs7761068 6:31333939 HLA-G 2.54 × 10−5 45.42
Pre-frontal cortex rs9267873 6:32199352 rs2247056 6:31265490 HLA-DRB5 2.19 × 10−8 83.34
  rs9267873 6:32199352 rs6457374 6:31272261 HLA-DRB5 2.74 × 10−8 83.10
  rs507778 6:32209861 rs6457374 6:31272261 HLA-DRB5 1.57 × 10−7 −80.99
  rs507778 6:32209861 rs2247056 6:31265490 HLA-DRB5 2.32 × 10−7 −79.75
  rs2072633 6:31919578 rs3093998 6:31485174 HLA-DRB5 1.05 × 10−7 74.74
  rs592229 6:31930441 rs3093998 6:31485174 HLA-DRB5 2.09 × 10−7 72.20
  rs805262 6:31628733 rs2247056 6:31265490 HLA-DRB5 2.34 × 10−6 −70.73
  rs805262 6:31628733 rs6457374 6:31272261 HLA-DRB5 3.10 × 10−6 −70.46
  rs2858331 6:32681277 rs3093998 6:31485174 HLA-DRB5 3.24 × 10−6 −67.31
  rs915664 6:30794617 rs3094212 6:31085770 HLA-G 6.56 × 10−7 63.74
  rs13201769 6:30756066 rs2524089 6:31266522 HLA-G 7.48 x 10−7 −60.37
  rs13201769 6:30756066 rs2243868 6:31261276 HLA-G 8.01 × 10−7 −60.38
  rs10947091 6:30747216 rs2524089 6:31266522 HLA-G 9.66 × 10−7 −60.94
  rs10947091 6:30747216 rs2243868 6:31261276 HLA-G 1.05 × 10−6 −60.91
  rs3869070 6:30023868 rs3093998 6:31485714 HLA-G 1.86 × 10−6 66.69
Cerebellum rs11744596 5:68519291 rs13168712 5:70679626 LOC100506658 1.52 × 10−6 −56.61
  rs2932777 5:68525027 rs13168712 5:70679626 LOC100506658 1.52 × 10−6 −56.61
  1. Table shows the interacting cis and trans SNP identifiers, positions and two-locus p-values for the Bonferroni significant interactions in three of the four tissues studied. Groups of dependent SNPs resulting from linkage disequilibrium amongst groups of cis-SNPs and groups of trans-SNPs are demarcated by a black horizontal line.