Table 1. Number (proportion) of SNPs classified as eQTLs for diseases with different focal tissues.
| Using eQTLs from CEU+YRI | # SNPs | eQTL p-value threshold 10−4 | eQTL p-value threshold 10−6 |
| Platform SNPs (MAF >.05) | 1,213,906 | 595,285 (.490) | 29,347 (.024) |
| All Catalog SNPs | 1598 | 972 (0.608) | 83 (0.052) |
| Autoimmune Disorders | 259 | 165 (0.637) | 21 (0.081) |
| Cancers | 93 | 56 (0.602) | 4 (0.043) |
| Neurological/Psychiatric Disorders | 63 | 41 (0.651) | 2 (0.032) |
| Using eQTLs from CEU only | |||
| Platform SNPs (MAF >.05) | 1,213,906 | 345,249 (.284) | 12,749 (.011) |
| All Catalog SNPs | 1598 | 625 (0.391) | 46 (0.029) |
| Autoimmune Disorders | 259 | 116 (0.448) | 17 (0.066) |
| Cancers | 93 | 30 (0.323) | 3 (.032) |
| Neurological/Psychiatric Disorders | 63 | 20 (0.317) | 1 (0.016) |
SNPs from the NHGRI catalog were classified according to the type of disease leading to their inclusion as a trait-associated SNP to investigate whether eQTLs identified in LCLs are more enriched in disorders for which LCLs are more likely to be an appropriate tissue match for the disease. Studies were conducted separately using eQTLs identified in the combined CEU+YRI samples (upper lines), and those identified only in the CEU (lower lines). Only SNPs with MAF >0.05 are included in these studies, and eQTL p-value thresholds of 10−4 and 10−6 are shown.