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Table 3 Comparison of colon cis -eQTL results with published studies in different tissues

From: Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci

  FDR
  Samples   0.01 0.05 0.10 0.20
LCL [41] 13,643 genes and ~2.2 million SNPs in 270 HapMap subjects (CEU, CHB, JPT and YRI populations) Genes* 25 (20%) 49 (14%) 72 (11%) 119 (7.4%)
SNP-gene pairs** 130 182 298 361
Liver [35] 34,266 genes and 782,476 SNPs in liver samples acquired from 427 Caucasian subjects Genes* 41 (34%) 95 (27%) 169 (25%) 346 (21%)
SNP-gene pairs** 8 15 20 33
Brain [48] 22,184 genes and 1,629,853 SNPs in brain tissue samples from 150 Caucasian subjects Genes* 17 (14%) 35 (9.9%) 63 (9.2%) 137 (8.5%)
SNP-gene pairs** 139 191 277 327
Skin [46] 14,500 genes and 438,670 SNPs in skin samples from 57 Caucasian subjects Genes* 24 (20%) 39 (11%) 59 (8.6%) 92 (5.7%)
SNP-gene pairs** 131 92 71 50
Ileum [49] 19,047 genes and 581,633 SNPs in ileum samples from 173 mostly Caucasian subjects Genes* 37 (30%) 83 (24%) 118 (17%) 197 (12%)
SNP-gene pairs** 176 130 94 58
  1. *The number of target genes from other studies overlapping colon cis-eQTL target genes are listed along with the percentages of overlap (in parentheses). To calculate the percentage of overlap, the number of overlapping target genes was divided by the total number of unique significant colon cis-eQTL target genes at the corresponding FDR threshold (refer to Table 1 for the actual numbers). **The number of SNP-gene pairs that overlap between the colon and other tissues.