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) | ||||||
| Â | 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) |