Study | Zeller et al27 | Dixon et al28 | Montgomery et al29 | Stranger et al30 | Dimas et al31 | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Population | 1490 German individuals | 206 families of British descent | 60 CEU individuals of the HapMap collection | 60 individuals of the HapMap collection CEU | 80 individuals of Western European origin | ||||||||
Gene | AVIL | XRCC6BP1 | TSFM | FAM119B | TSPAN31 | FAM119B | TSFM | CYP27B1 | FAM119B | FAM119B | FAM119B | FAM119B | FAM119B |
Cell type | Monocytes | LCL | LCL | LCL | T-cells | LCL | Fibroblasts | ||||||
Probe/Transcript | ILMN_20148 | ILMN_16915 | ILMN_27946 | ILMN_12426 | ILMN_11441 | 213861_s_at | 212656_at | ENST00000228606 | ENST00000300209 | GI_24308058-S | ILMN_1723846 | ILMN_1723846 | ILMN_1723846 |
p Value/effect | p Value/effect | p Value/effect | p Value/effect | p Value | |||||||||
SNP | |||||||||||||
rs6581155 | 2.1E−10/−0.57 | ||||||||||||
rs10747783 | 5.00E−21/−0.731 | 9.00E−13/0.564 | 7.5E−11/−0.58 | ||||||||||
rs923829 | 5.00E−21/−0.731 | 9.00E−13/0.564 | 6E−11/−0.58 | ||||||||||
rs10431552 | 2.80E−21/−0.745 | 1.00E−12/0.569 | 2.1E−10/−0.57 | ||||||||||
rs2072052 | 7.70E−19/−689 | 1.00E−13/0.588 | 5E−10/−0.56 | ||||||||||
rs2291617 | 4.10E−11/−0.62 | 7.60E−11/0.626 | 6E−11/−0.58 | ||||||||||
rs4646536 | 1.7E−07/−0.021 | 5E−38/0.11 | 7.71E−19/0.055 | 3.34E−236/−0.52 | 1.4E−11/0.033 | 2.1E−10/−0.57 | |||||||
rs724834 | 6E−11/−0.58 | ||||||||||||
rs2069502 | 1.84E−08/−0.024 | 4.4E−38/0.11 | 6.19E−17/0.049 | 7.78E−221/−0.5 | 2.29E−12/0.036 | 7.7E−19/−0.689 | 1.40E−13/0.583 | 5.3E−10/−0.56 | |||||
rs10877013 | 8.80E−20/−0.711 | 1.80E−12/0.56 | 4.1E−10/−0.56 | 0.000012/−0.481 | 0.000292/−0.407 | 0.0000001/−0.571 | |||||||
rs10877011 | 8.90E−14/−0.612 | 9.00E−13/0.6 | 0.00014157/−0.472 | 0.00013264/−0.474 | 9.5E−11/−0.57 | ||||||||
rs701008 | 2.30E−12/−0.563 | 2.30E−11/0.55 | 1.6E−8/−0.51 | ||||||||||
rs8181644 | 1.2E−07/−0.022 | 3.8E−38/0.11 | 1.4E−19/0.057 | 3.9E−234/−0.52 | 5.5E−12/0.034 | 2.1E−10/−0.57 | |||||||
rs10877019 | 4.2E−07/−0.023 | 6.31E−38/0.11 | 1.024E−190.058 | 8.32E−233/−0.52 | 1.52E−11/0.034 | 2.1E−10/−0.57 | |||||||
rs11172335 | 2.1E−10/−0.57 | ||||||||||||
rs703842 | 1.67E−07/−0.021 | 2.42E−37/0.11 | 1.42E−18/0.054 | 7.5E−235/−0.52 | 1.41E−11/0.037 | 7.80E−17/−0.694 | 2.50E−11/0.568 | 2.1E−10/−0.57 | |||||
rs10877015 | 2.1E−10/−0.57 | ||||||||||||
rs11172333 | 1.11E−07/−0.023 | 7.31E−39/0.11 | 1.74E−19/0.057 | 2.07E−233/−0.51 | 5.63E−12/0.035 | 2.1E−10/−0.57 |
Zeller et al Genome-Wide Expression analysis performed with Illumina HT-12 v3 BeadChip. Association significance was obtained by ANalysis Of VAriance (ANOVA).
Dixon et al Genome-Wide Expression analysis performed by U133 Plus 2.0 GeneChips (Affymetrix). Association analysis was obtained by fitting a simple regression model to each trait and used a variance component approach to account for correlation between different observed phenotypes within each family.
Montgomery et al Genome-Wide Expression analysis performed by RNA sequencing in an Illumina GAII. Association analysis and multiple testing corrections were conducted by spearman rank correlation and permuting the expression phenotype 10 000 times and summarising the extreme p value distribution for each particular exon, transcript and probe.
Stranger et al Genome-Wide Expression analysis performed with Sentrix Human-6 Expression BeadChip V.1, Illumina. Association significance was obtained by spearman rank correlation with 10 000 permutations of the expression phenotypes.
Dimas et al Gene expression was performed by commercial whole-genome expression array (WG-6 V.3 Expression BeadChip, Illumina). Association analysis and multiple testing corrections were conducted by spearman rank correlation. Thresholds for each gene were assigned after 10 000 permutations of expression values relative to genotypes where the haplotypic (LD) structure was maintained in each interaction.
eQTL, expression quantitative trait loci; LCL, lymphoblastic cell lines.