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

Table 3 SNPs that map to promoter regions in brain tissues

Tissue	Pre-frontal cortex				Cerebellum				Visual cortex
	Epistatic	Non-epistatic	OR	P-value	Epistatic	Non-epistatic	OR	P-value	Epistatic	Non-epistatic	OR	P-value
AC	19/258	506/19335	2.95	6.9 × 10⁻⁶ *	14/151	403/15883	3.93	9.75 × 10⁻⁷*	1/73	282/11304	0.35	0.14
HM150	18/258	463/19335	3.1	6.12 × 10⁻⁶*	14/151	372/15883	4.26	1.42 × 10⁻⁷*	3/73	265/11304	0.9	0.99
AG	13/258	424/19335	2.37	0.004	11/151	358/15883	3.41	0.00013*	3/73	251/11304	0.45	0.24
ITL	13/258	465/19335	2.15	0.012	13/151	372/15883	3.92	2.14 × 10⁻⁶*	3/73	273/11304	0.46	0.26
GM2	10/258	381/19335	2	0.05	9/151	326/15883	3.02	0.002	2/73	226/11304	1.02	1
MFL	15/258	421/19335	2.77	0.0002	12/151	349/15883	3.84	8.02 × 10⁻⁶*	3/73	250/11304	0.37	0.22
SN	15/258	485/19335	2.4	0.002	13/151	313/15883	4.69	4.68 × 10⁻⁸*	3/73	237/11304	0.7	0.64

SNPs that map to promoter regions as measured in 7 brain tissues by the Roadmap Epigenomics Project and mined from HaploReg are given as the proportion of SNPs that map to such regions for the set of SNPs involved in epistatic interactions and those not involved in interactions. The odds ratio (OR) that a SNP involved in an epistatic interaction will also be in an enhancer region is given. Significance is assessed using a chi-squared test for goodness of fit. Tissues with a significant enrichment of promoter mappings after Bonferroni correction for multiple testing (P < 2.4 × 10–3) are denoted with an asterisk (*).
AC – Anterior Caudate; HM150 – Hippocampus Middle; AG – Angular Gyrus; ITL – Inferior Temporal Lobe; GM2 - Germinal Matrix; MFL – Mid Frontal Lobe; SN – Substantia Nigra.

ISSN: 1471-2164