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Table 1 Genetic associations with NMR intensities and ratios between NMR intensities.

From: Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

Locus SNP CHRa POSa Aa Ba MAF Chemical shift(ppm) n Beta'b P value Chemical shifts for ratios (ppm) n Beta' ratiosb P value ratios P gainc
GCKR rs780094 2 27,594,741 T C 41.4% 1.370 1,688 0.0413 1.2x10-10 3.286/1.370 1,667 -0.0407 2.8x10-15 4.3x104
CPS1 rs2216405 2 211,325,139 C T 19.3% 3.599 1,719 0.0456 4.5x10-14 3.599/2.475 1,718 0.0459 1.8x10-19 2.5x105
PYROXD2 rs4488133 10 100,149,126 A T 34.3% 2.757 1,735 -0.0190 7.3x10-12 2.757/2.755 1,734 -0.0123 2.9x10-94 2.5x1082
FADS1 rs174547 11 61,327,359 C T 30.0% 2.801 1,733 -0.0408 4.0x10-35 2.801/2.017 1,724 -0.0449 1.1x10-94 3.8x1059
APOA1 rs3741298 11 116,162,771 C T 21.4% 2.038 1,724 0.0363 8.4x10-11 4.162/4.082 1,715 -0.0138 1.8x10-14 4.6x103
LIPC rs4775041 15 56,461,987 C G 28.5% 1.283 1,671 0.0320 1.4x10-10 1.068/1.029 1,664 -0.0056 3.6x10-21 4.0x1010
CETP rs247617 16 55,548,217 A C 31.3% 3.259 1,705 0.0529 7.6x10-15 2.211/2.011 1,695 -0.0124 1.1x10-18 6.8x103
  1. The locus name indicates the gene that most likely hosts the causative SNP.
  2. A/B: minor/major allele; MAF: minor allele frequency; n: number of samples where genetic and NMR data are jointly available; ppm: parts per million.
  3. aChromosomal location (CHR, POS), minor (effect, A) and major (B) alleles are reported with respect to the positive strand of the human genome (NCBI build 36.1).
  4. bBeta': relative effect size, defined as beta' = (10beta- 1), where beta is the slope in the linear model (using log10-scaled traits) and genotype is coded as 0-1-2 (major-hetero-minor genotype). Beta' represents the relative difference per copy of the minor allele for the unscaled metabolic trait (NMR bin or NMR ratio) compared to the estimated mean of the major allele homozygote group (intercept of the linear model).
  5. cThe P gain is defined as min(p(S1)/p(S1/S2), p(S2)/p(S1/S2)), where p(S1), p(S2), and p(S1/S2) denote the P values of association of two log-scaled NMR intensities at chemical shift S1 and S2, and of their ratio S1/S2, respectively.