Skip to main content

Table 4 SNPs that map to enhancer 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 23/258 1547/19335 1.12 0.67 12/151 1364/15883 1.67 0.03 3/73 928/11304 0.32 0.14
HM150 20/258 1387/19335 1.1 0.8 7/151 1200/15883 1.6 0.07 5/73 856/11304 0.9 0.99
AG 24/258 1649/19335 1.1 0.74 9/151 1439/15883 1.63 0.04 3/73 980/11304 0.45 0.24
ITL 21/258 1605/19335 0.98 1 8/151 1427/15883 0.57 0.15 3/73 959/11304 0.46 0.26
GM2 11/258 816/19335 1.01 1 5/151 702/15883 0.74 0.64 3/73 455/11304 1.02 1
MFL 14/258 1401/19335 0.73 0.32 3/151 1219/15883 0.24 0.01 2/73 802/11304 0.37 0.22
SN 26/258 1362/19335 1.48 0.08 6/151 1262/15883 0.48 0.1 4/73 857/11304 0.7 0.64
  1. SNPs that map to enhancer 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. SNPs involved in epistatic interactions are not enriched for enhancer mappings in any of the 7 brain tissues.
  2. AC – Anterior Caudate; HM150 – Hippocampus Middle; AG – Angular Gyrus; ITL – Inferior Temporal Lobe; GM2 - Germinal Matrix; MFL – Mid Frontal Lobe; SN – Substantia Nigra.