Table 1. eQTLs with a nominally significant GWAS p value in the replication data.
| Locus | Chr | Illumina HT-12v3 probe identifier | Clump index SNP | Minor allele | GWAS discovery SNP association | GWAS replication SNP association | Joint GWAS SNP association | eQTL p value after permutations | eQTL direction of effect | |||||
| OR | p | OR | p | p bonf. | OR | p | Discovery | Replication | ||||||
| CYP27A1 | 2 | ILMN_1704985 | rs4674345 | G | 1.08 | 0.049 | 1.23 | 1.32×10−4 | 0.042 | 1.12 | 1.84×10−4 | 1.65×10−46 | 1.19×10−47 | + |
| CENPV | 17 | ILMN_1729142 | rs10491104 | G | 1.11 | 3.79×10−3 | 1.17 | 3.64×10−3 | n.s. | 1.14 | 2.35×10−5 | 1.15×10−5 | 9.50×10−4 | + |
| SLC11A1 | 2 | ILMN_1741165, ILMN_1735737 | rs2279014 | A | 1.12 | 2.26×10−3 | 1.15 | 0.011 | n.s. | 1.13 | 4.98×10−5 | 5.48×10−27 | 7.49×10−40 | + |
| TTC39C | 18 | ILMN_1746720 | rs1154227 | G | 1.08 | 0.037 | 1.15 | 0.011 | n.s. | 1.12 | 3.00×10−4 | 6.23×10−6 | 5.25×10−4 | + |
| SPI1, MYBPC3 | 11 | ILMN_1696463, ILMN_1781184 | rs7126210 | A | 1.08 | 0.044 | 1.15 | 0.021 | n.s. | 1.11 | 2.28×10−3 | 5.44×10−9 | 1.57×10−5 | + |
| RABEP1 | 17 | ILMN_1719622 | rs3865351 | A | 0.91 | 0.024 | 0.88 | 0.021 | n.s. | 0.90 | 2.06×10−3 | 2.70×10−7 | 1.19×10−6 | + |
| ZNF586 | 19 | ILMN_2372200 | rs4801516 | A | 0.92 | 0.020 | 0.89 | 0.027 | n.s. | 0.92 | 8.15×10−3 | 6.73×10−5 | 3.60×10−3 | + |
| KIAA0513 | 16 | ILMN_1693233 | rs8056742 | G | 1.17 | 7.51×10−3 | 1.19 | 0.029 | n.s. | 1.19 | 1.42×10−4 | 4.29×10−8 | 6.44×10−15 | + |
| C17orf75, CDK5R1 | 17 | ILMN_1797155, ILMN_1730928 | rs4795700 | A | 1.12 | 2.15×10−3 | 1.12 | 0.034 | n.s. | 1.11 | 4.14×10−4 | 3.33×10−26 | 9.85×10−40 | + |
| SLC39A1 | 1 | ILMN_2116714 | rs11264743 | A | 0.92 | 0.032 | 0.88 | 0.035 | n.s. | 0.91 | 2.72×10−3 | 9.47×10−7 | 2.09×10−4 | + |
| Hs.447737 | 5 | ILMN_1896967 | rs13354021 | G | 0.92 | 0.040 | 0.89 | 0.040 | n.s. | 0.91 | 3.46×10−3 | 3.05×10−7 | 1.51×10−4 | + |
| CLEC12A | 12 | ILMN_1663142, ILMN_2292178 | rs10505745 | A | 1.16 | 1.91×10−3 | 1.14 | 0.049 | n.s. | 1.14 | 5.75×10−4 | 5.09×10−5 | 6.81×10−5 | – |
Independent eQTLs are based on LD-based SNP clumping. For each locus, the clump index SNP (with the lowest p value) is shown. For the GWAS replication results, Bonferroni corrected p values are given for the testing of 322 clumps. SNP association results in the joint GWAS data were based on a total of 3,568 ALS patients and 10,163 controls. For the eQTL direction of effect, ‘+’ means the SNP minor allele was associated with increased expression levels, ‘–’ means decreased gene expression. Chr, chromosome; LD, linkage disequilibrium; GWAS, genome-wide association study; OR, odds ratio; p bonf., Bonferroni corrected p value; n.s., not significant; eQTL, expression quantitative trait locus.