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Table 1 Summary of cis-eQTL findings from celiac peripheral blood and HapMap B cell line data sets

From: Complex nature of SNP genotype effects on gene expression in primary human leucocytes

Population 110 celiac disease samples
(Celiac peripheral blood dataset)
90 Caucasian HapMap samples
(HapMap B cell datasets)
Expression data Illumina HumanRef-8 v2 Whole
Genome BeadChip (19,867 mapped transcripts)
Illumina HumanRef-6 v1 Whole
Genome BeadChip (44,791 mapped transcripts)
Genotype data Illumina Infinium HumanHap300 BeadChip (257,013 SNPs assessed) Subset of all HapMap Genotypes present on Illumina Infinium HumanHap300 BeadChip (257,013 SNPs assessed)
  FDR 0.01 FDR 0.05 FDR 0.01 FDR 0.05
SNP-Probe midpoint distance 250 kb 500 kb 250 kb 500 kb 250 kb 500 kb 250 kb 500 kb
FDR Spearman's Correlation P-Value Threshold p < 1.67 × 10-5 p < 6.57 × 10-6 p < 1.36 × 10-4 p < 5.47 × 10-5 p < 1.08 × 10-5 p < 4.20 × 10-6 p < 8.79 × 10-5 p < 3.47 × 10-5
Number of performed tests 930,456 1,850,599 930,456 1,850,599 1,913,342 3,820,148 1,913,342 3,820,148
Number of detected different
SNP-probe effects
1,529 (235) 1,360 (233) 2,487 (372) 2,178 (355) 1,981 (664) 1,799 (623) 3,226 (1,068) 2,839 (988)
Number of unique probes 470 (65) 394 (56) 765 (98) 658 (84) 613 (193) 536 (177) 994 (289) 821 (255)
Number of unique genes 460 (65) 385 (56) 753 (98) 647 (84) 563 (189) 491 (174) 903 (277) 746 (244)
Number of unique SNPs 1,432 (234) 1,273 (230) 2,315 (367) 2,035 (345) 1,743 (628) 1,601 (585) 2,826 (1009) 2,464 (920)
  1. Numbers within brackets denote the number of cis-eQTLs, probes or genes that are potentially due to SNPs that map within the probe and affect the hybridization efficacies of these probes.