Table 2.
Meta‐Analysis Identifies 12 Loci Significantly Associated With Circulating Glycine Levels
| Locus (Nearest Gene(s))a | Lead SNP | Position (bp)b | Effect/Other Allelec | EAF | β (SE) | P Value | Directiond |
|---|---|---|---|---|---|---|---|
| 1p31.1 (ACADM) | rs12126607 | 76 217 097 | A/G | 0.27 | 0.06 (0.01) | 1.1×10−11 | +−++ |
| 1p12 (PHGDH) | rs478093 | 120 255 126 | G/A | 0.67 | 0.06 (0.01) | 3.5×10−10 | ++++ |
| 2q34 (CPS1) | rs1047891 | 211 540 507 | A/C | 0.34 | 0.43 (0.01) | <1.0×10−300 | ++++ |
| 3q21.3 (ALDH1L1) | rs2364368 | 125 905 080 | T/A | 0.40 | 0.09 (0.01) | 2.2×10−28 | ++++ |
| 4q13.3 (COX18‐ADAMTS3) | rs143424675 | 73 749 419 | T/C | 0.03 | 0.19 (0.03) | 7.3×10−13 | +−++ |
| 7p11.2 (PSPH) | rs6955423 | 56 099 352 | A/G | 0.81 | 0.07 (0.01) | 2.3×10−11 | ++++ |
| 8p23.1 (PPP1R3B‐LOC157273) | rs2126263 | 9 181 611 | G/A | 0.15 | 0.16 (0.01) | 5.8×10−44 | ++++ |
| 8q24.13 (TRIB1) | rs28601761 | 126 500 031 | G/C | 0.41 | 0.06 (0.01) | 1.6×10−13 | +−++ |
| 9p24.1 (GLDC) | rs71503800 | 6 102 648 | T/C | 0.05 | 0.46 (0.02) | 8.5×10−121 | −++ |
| 9p24.1 (PTPRD) | rs12003835 | 8 424 378 | T/G | 0.03 | 0.15 (0.03) | 8.2×10−9 | −++ |
| 9q34.2 (ABO)e | rs492488 | 136 144 960 | G/A | 0.55 | 0.05 (0.01) | 1.2×10−8 | −+++ |
| 16q23.2 (GCSH) | rs11860711 | 81 132 493 | C/T | 0.80 | 0.12 (0.01) | 4.2×10−31 | ++++ |
EAF indicates effect allele frequency; SNP, single‐nucleotide polymorphism.
a
Novel loci identified in this study are highlighted in gray.
b
SNP base pair (bp) positions are given according to NCBI build 37 of the reference human genome sequence (hg19).
c
Effect allele refers to allele that increases glycine levels.
d
Direction of betas in the 4 data sets used for meta‐analysis are in the following order: GB I, GB II, Combination of FR97‐FR07‐YFS‐NFBC66‐NFBC86, and METSIM.
e
N=27 006 for chromosome 9q34.2 locus.