Table 3. Nine SLE loci contain cis-eQTLs driven by the same variant as the disease association.
| Gene | Transcript | Exon | Junction | Intron | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Lead SNP | Gene | eQTL Pa | JLIM P | eQTL P | JLIM P | eQTL P | JLIM P | eQTL P | JLIM P | eQTL P | JLIM P |
| rs2476601 | PHTF1 | - | - | 2.2 x 10−3 | 6.2 x 10−1 | 5.0 x 10−8 | 1 | 8.4 x 10−47 | 1 | 1.4 x 10−4 | 1.0 x 10−4 |
| rs1801274 | ARHGAP30 | 2.4 x 10−6 | 8.1 x 10−1 | - | - | 1.1 x 10−4 | 2.0 x 10−4 | 9.4 x 10−3 | 7.4 x 10−3 | 1.2 x 10−3 | 4.8 x 10−1 |
| rs9782955 | LYST | 5.4 x 10−3 | 3.90 x 10−1 | 8.0 x 10−6 | 9.8 x 10−1 | 1.6 x 10−3 | 4.6 x 10−3 | 1.3 x 10−3 | 2.0 x 10−4 | 1.0 x 10−5 | 5.0 x 10−1 |
| rs3768792 | IKZF2 | - | - | 1.5 x 10−3 | 7.7 x 10−1 | 1.9 x 10−4 | 3.0 x 10−4 | 1.0 x 10−5 | 9.0 x 10−1 | 1.1 x 10−5 | 2.0 x 10−4 |
| rs10028805 | BANK1 | 1.8 x 10−3 | 3.1 x 10−3 | 4.9 x 10−3 | 3.2 x 10−3 | 1.8 x 10−5 | 4.0 x 10−4 | 2.5 x 10−4 | 2.0 x 10−4 | 1.8 x 10−4 | 9.7 x 10−1 |
| rs2736340 | BLK | 3.2 x 10−26 | < 10−4 | 1.0 x 10−9 | < 10−4 | 1.4 x 10−31 | < 10−4 | 7.6 x 10−28 | < 10−4 | 3.1 x 10−24 | < 10−4 |
| FAM167A | 2.3 x 10−40 | < 10−4 | 4.4 x 10−45 | < 10−4 | 5.1 x 10−46 | < 10−4 | 1.5 x 10−22 | < 10−4 | 7.4 x 10−15 | < 10−4 | |
| rs2286672 | RABEP1 | 1.4 x 10−3 | 5.1 x 10−2 | 1.3 x 10−4 | 9.4 x 10−1 | 7.4 x 10−5 | 4.0 x 10−4 | 4.5 x 10−4 | 7.0 x 10−4 | 1.3 x 10−4 | 8.5 x 10−1 |
| rs2304256 | TYK2 | 1.2 x 10−3 | 7.6 x 10−1 | 9.9 x 10−6 | 9.9 x 10−1 | 2.5 x 10−9 | < 10−4 | 1.3 x 10−4 | 3.0 x 10−3 | 2.2 x 10−9 | 2.0 x 10−4 |
| ATG4D | - | - | 3.8 x 10−3 | 7.2 x 10−3 | 6.4 x 10−5 | 3.8 x 10−3 | 3.8 x 10−4 | 2.0 x 10−4 | 6.6 x 10−5 | 9.7 x 10−1 | |
| rs7444 | UBE2L3 | 5.7 x 10−3 | 2.0 x 10−1 | 5.9 x 10−14 | < 10−4 | 9.9 x 10−5 | < 10−4 | 5.1 x 10−5 | 9.5 x 10−1 | 1.2 x 10−3 | 9.0 x 10−1 |
| CCDC116 | 2.5 x 10−5 | 5.0 x 10−4 | 1.4 x 10−6 | 3.0 x 10−4 | 4.9 x 10−4 | 4.0 x 10−4 | - | - | - | - | |
Nine of the 38 SLE loci (24%) were found to be driven by the same causal variant as the disease association across all five RNA-Seq quantification types in LCLs (cis-eQTL P<0.01 and joint likelihood of shared association FDR<0.05). Bold type indicates associations that show evidence of a shared causal variant for cis-eQTL and disease.
aMinimum cis-eQTL P-value for any SNP within 100 kb of the lead SNP. Dashes (–) indicate genes that were either not detected or had minimum cis-eQTL P>0.01 in the RNA-Seq quantification type in hand. JLIM P-values <10−4 indicates the JLIM statistic is more extreme than permutation. JLIM: joint likelihood mapping. If multiple SNP-unit associations are deemed to be causal (i.e. one SNP shows a causal association to two exons of the same gene, the association with the smallest JLIM P-value is reported).