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Table 3 SNPs that map to promoter regions in brain tissues

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

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
  1. 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 (*).
  2. AC – Anterior Caudate; HM150 – Hippocampus Middle; AG – Angular Gyrus; ITL – Inferior Temporal Lobe; GM2 - Germinal Matrix; MFL – Mid Frontal Lobe; SN – Substantia Nigra.