Table 1.

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

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

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.