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. 2020 Dec 19;12(12):3890. doi: 10.3390/nu12123890

Table 2.

Independent GWAS hits at suggestive significance p < 1.11 × 10−6 per amino acid trait in EPIC-Potsdam.

Amino Acid Trait SNP SNP Coordinates Gene EA/OA EAF N Beta (SE) p-Value Consequence (GRCH37) CADD-Score [40]
Glycine/Serine rs1047891 2:211540507 CPS1 A/C 0.31 2265 0.50 (0.03) 7.58 × 10−54 Thr1406Asn 22.1
rs2010825 7:44188220 GCK C/T 0.51 2265 0.15 (0.03) 5.78 × 10−7 Downstream gene variant 5.97
rs561931 1:120254506 PHGDH G/A 0.61 2265 −0.18 (0.03) 2.28 × 10−9 Upstream gene variant 7.61
rs9851577 3:125908310 ALDH1L1; ALDH1L1-AS2 T/C 0.46 2265 0.15 (0.03) 7.36 × 10−7 Intron variant 2.44
Glycine rs1047891 2:211540507 CPS1 A/C 0.31 2264 0.59 (0.03) 2.79 × 10−76 Thr1406Asn 22.1
rs61992673 14:101542105 AL132709.1; MEG9 A/C 0.20 2264 −0.22 (0.04) 1.62 × 10−8 Intron variant 5.34
Phenylalanine/ rs1451722 11:3856553 RHOG T/C 0.58 2265 −0.15 (0.03) 3.51 × 10−7 Intron variant 12.7
Arginine rs1718309 12:103242396 PAH G/A 0.60 2265 −0.17 (0.03) 3.44 × 10−8 Intron variant 3.32
Phenylalanine rs55940357 19:2610628 GNG7; CTC-265F19.2 C/T 0.88 2265 0.24 (0.05) 1.03 × 10−6 Intron variant 1.72
Serine/ rs1047891 2:211540507 CPS1 A/C 0.31 2265 0.18 (0.03) 5.95 × 10−8 Thr1406Asn 22.1
Phenylalanine rs11024310 11:17520786 USH1C G/C 0.08 2265 −0.31 (0.06) 9.83 × 10−7 Intron variant 1.25
rs2992975 1:194106746 - A/G 0.41 2265 0.17 (0.03) 5.65 × 10−7 Intergenic variant 0.63
rs478093 1:120255126 PHGDH G/A 0.69 2265 0.18 (0.03) 1.27 × 10−8 Intron variant 8.15
Tryptophan/ rs4903067 14:73286300 DPF3 C/T 0.34 2260 −0.15 (0.03) 6.28 × 10−7 Intron variant 0.88
Glutamine rs7973936 12:64333645 SRGAP1 A/G 0.31 2260 0.18 (0.03) 3.07 × 10−8 Intron variant 1.58
Tyrosine/ rs12756904 1:104337030 - C/T 0.20 2261 −0.18 (0.04) 1.08 × 10−6 Intergenic variant 2.96
Methionine rs17606481 6:111542388 SLC16A10 G/A 0.15 2261 0.28 (0.04) 1.70 × 10−11 Intron variant 2.49
rs72792419 16:58741949 GOT2 C/T 0.08 2261 −0.30 (0.06) 6.59 × 10−7 Downstream gene variant 4.23
Valine/xLeucine rs2456586 19:51434353 CTB-147C22.3 C/T 0.39 2258 0.15 (0.03) 6.11 × 10−7 Upstream gene variant 0.64
xLeucine/ rs12642299 4:90942633 - G/C 0.67 2263 0.17 (0.03) 6.16 × 10−8 Intergenic variant 0.99
Methionine rs1958029 14:21491151 NDRG2; AL161668.5; TPPP2 G/A 0.11 2263 −0.25 (0.05) 1.84 × 10−7 Upstream gene variant 3.12

CADD, combined annotation dependent depletion; EA, effect allele; EAF, effect allele frequency; OA, other allele; SE, standard error. SNP, single nucleotide polymorphism.