Table 1. Top 10 association signals in the GGRI TS GWAS follow-up study (609 cases and 610 ancestry-matched controls).
Results of the original TS GWAS for these top linkage disequilibrium (LD)-independent SNPs as well as results of a meta-analysis of the replication and prior GWAS sample (total of 1894 cases and 5574 controls) are also shown. The closest genes around each SNP of interest and association with gene expression and/or methylation levels in cerebellar or frontal cortex tissue are also indicated.
| TS GWAS | GGRI sample | Meta-analysis | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHR | SNP | BP (hg19) | A1/A2 | MAF | OR | P | OR | P | OR | P | Gene | eQTL/mQTL |
| 12 | rs2060546 | 96,215,456 | A/G | 0.027 | 1.60 | 3.7×10−4 | 2.41 | 3.3×10−4 | 1.77 | 5.8×10−7 | SNRPF|NTN4|CCDC38 | |
| 2 | rs1922786 | 58,863,573 | G/A | 0.35 | 0.83 | 2.1×10−4 | 0.76 | 2.4×10−3 | 0.81 | 1.9×10−6 | SEL1L2, LMAN1L, INSL3 | |
| 9 | rs7868992 | 116,991,071 | G/A | 0.28 | 1.29 | 1.9×10−6 | 1.11 | 0.26 | 1.24 | 6.4×10−6 | COL27A1 | SYTL4, AMBP, HSPC152, OAS2, PWP1, RALBP1 |
| 11 | rs11603305 | 10,997,949 | G/A | 0.28 | 1.27 | 1.3×10−5 | 1.16 | 0.10 | 1.24 | 7.2×10−6 | ||
| 7 | rs1882078 | 37,436,975 | C/T | 0.28 | 1.27 | 1.9×10−5 | 1.15 | 0.11 | 1.23 | 1.1×10−5 | ELMO1 | |
| 12 | rs6539267 | 106,785,554 | C/T | 0.31 | 0.79 | 7.4×10−6 | 0.90 | 0.22 | 0.82 | 1.1×10−5 | TCP11L2|POLR3B | TMEM119 |
| 7 | rs769111 | 12,059,806 | G/T | 0.38 | 0.81 | 1.2×10−5 | 0.90 | 0.19 | 0.83 | 1.6×10−5 | MEOX2, PLSCR1, PCDHB16 | |
| 11 | rs7123010 | 86,341,186 | A/G | 0.30 | 0.79 | 4.2×10−5 | 0.89 | 0.20 | 0.82 | 4.9×10−5 | ME3 | NFKBIZ, FLJ23514, KLF8, PICALM |
| 11 | rs621942 | 85,783,738 | A/C | 0.24 | 1.23 | 1.3×10−4 | 1.15 | 0.14 | 1.21 | 6.8×10−5 | PICALM | TMEM126B, TMEM126A, PICALM, CREB3L3, LRRC2 |
| 3 | rs2282755 | 50,442,800 | T/G | 0.28 | 0.80 | 5.6×10−5 | 0.90 | 0.24 | 0.82 | 7×10−5 | TMEM115|CACNA2D2 | ZMYND10, PTH1R, HYAL3, SEMA3G |
CHR, Chromosome; BP (hg19), Physical position according to NCBI Build 37/hg19 genome assembly; A1/A2, Allele 1/Allele 2 (Allele 1 is the minor allele); MAF, Minor Allele Frequency; OR, odds ratio; P, p-value of genetic association test; eQTL/mQTL, SNP associated with gene expression levels (cerebellum or frontal cortex) and/or methylation levels in cerebellum (as described in Scharf et al. 2013). Complete results of all 42 targeted SNPs are provided in Table S3.