Table 1.
Genome-wide significant associations with MacTel.
| Rsid | Chr | BP | Effect/non-effect allele | EAF cases | EAF controls | Cytoband | Odds ratio | 95% CI | P value | P value Eur | Proximal coding genes* | Scerri et al., 2017 GWAS | Bonelli et al., conditional GWAS |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs146953046 | 1 | 120278072 | G/T | 0.059 | 0.016 | p12 | 5.47 | 3.87–7.74 | 7.90 × 10−22 | 1.30 × 10−20 | PHGDH; HMGCS2 | – | – |
| rs532303 | 1 | 120265444 | G/A | 0.576 | 0.685 | p12 | 0.585 | 0.52–0.65 | 9.29 × 10−18* | 1.75 × 10−16* | PHGDH; HMGCS2 | GW | – |
| rs2160387 | 2 | 65220910 | C/T | 0.351 | 0.441 | p14 | 0.72 | 0.65–0.81 | 5.90 × 10−09 | 3.70 × 10−09 | SLC1A4 | – | – |
| rs1047891 | 2 | 211540507 | A/C | 0.192 | 0.306 | q34 | 0.56 | 0.5–0.63 | 8.60 × 10−21 | 3.60 × 10−20 | CPS1 | GW | – |
| rs9820465 | 3 | 27706298 | C/T | 0.145 | 0.205 | p24.1 | 0.66 | 0.57–0.76 | 5.60 × 10−09 | 1.50 × 10−07 | SLC4A7; EOMES | S | GW |
| rs17279437 | 3 | 45814094 | A/G | 0.144 | 0.104 | p21.31 | 1.73 | 1.45–2.06 | 6.20 × 10−10 | 9.70 × 10−10 | SLC6A20; SACM1L; LIMD1; LARS2 | – | – |
| rs17421627 | 5 | 87847586 | G/T | 0.132 | 0.069 | q14.3 | 2.31 | 1.9–2.81 | 4.70 × 10−17 | 1.00 × 10−16 | TMEM161B | GW | GW |
| rs6955423 | 7 | 56099352 | A/G | 0.651 | 0.746 | p11.2 | 0.7 | 0.62–0.79 | 5.90 × 10−09 | 2.60 × 10−07 | SEPT14;MRPS17;ZNF713;GBAS;PSPH;CCT6A;SUMF2;PHKG1;CHCHD2;NUPR1L | S | – |
| rs677622 | 9 | 15302613 | G/A | 0.821 | 0.869 | p22.3 | 0.63 | 0.54–0.73 | 3.20 × 10−09 | 1.10 × 10−09 | TTC39B | S | – |
| rs10995566 | 10 | 65363166 | T/C | 0.231 | 0.316 | q21.3 | 0.72 | 0.64–0.81 | 4.80 × 10−08 | 8.80 × 10−08 | NRBF2;JMJD1C;REEP3 | S | – |
| rs139412173 | 19 | 8235251 | G/A | 0.024 | 0.056 | p13.2 | 0.47 | 0.36–0.61 | 2.90 × 10−08 | 3.40 × 10−07 | CERS4, FBN3 | S Nearby | GW |
Top tagging GW-significant SNPs for each locus and relevant candidate genes from GWAS analysis. Bold text indicates the gene is covered by the haplotype (as defined by FUMA, based on linkage disequilibrium using the 1000 Genomes Project European cohort). Non-bold text indicates genes proximal to the locus. The Bonelli et al. GWAS7 was conditioned on genetically predicted T2D risk, and serum glycine and serine. Chr chromosome number, BP base pairs (Hg19 build), EAF effect allele frequency, CI confidence interval, Eur European-only sample subset, GW, genome-wide significant (P < 5 × 10−8), S suggestive significant (P < 5 × 10−6). This table is duplicated in Supplementary Data 17. *P values are conditional on SNP rs146953046 (non-conditional P values in all ancestry/euro analyses: 2.38 × 10−20/5.49 × 10−19).