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. 2022 Apr 4;130(4):047001. doi: 10.1289/EHP10174

Table 3.

Differentially methylated probes (DMPs) associated with urinary glyphosate and AMPA concentration in 332 postmenopausal California women.

Probe Freq. Median p-value Median FDR q-value Methylation (β) difference per unit glyphosate/AMPA Chr. Position (hg19) Gene(s) Gene summary Location within gene(s) CpG Island Predicted chromatin state
Glyphosate
 cg13499896 1,000 1.74×10−8 0.006 −0.71 22 18,571,657 PEX26 Probably required for protein import into peroxisomes. 3’UTR Open Sea Strong enhancer
 cg24576174 1,000 4.24×10−8 0.010 −0.60 11 65,828,083 SF3B2 Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex. Body Open Sea Transcription elongation
 cg00355690 996 5.64×10−8 0.011 −1.89 16 89,722,417 CHMP1A Involved in multivesicular body sorting of proteins to the interiors of lysosome. Involved in cytokinesis. May also be involved in chromosome condensation. May play a role in stable cell cycle progression and in PcG gene silencing. Body N. Shore Weak enhancer
 cg26833395 1,000 5.76×10−8 0.012 −0.11 20 30,102,102 HM13 Plays a key role in generating signal sequence-derived human lymphocyte antigen-E epitopes that are recognized by the immune system. Promoter Island Weak promoter
 cg06993862 987 2.62×10−7 0.023 −2.25 3 49,141,001 QARS1 Plays a critical role in brain development. Body N. Shore Strong enhancer
 cg13310154 978 4.56×10−7 0.029 −0.11 17 55,910,843 — — Intergenic Open Sea Insulator
 cg16601151 959 5.92×10−7 0.031 −0.11 16 19,079,341 COQ7 Involved in ubiquinone biosynthesis. Involved in lifespan determination in a ubiquinone-independent manner. Body Island Active promoter
 cg26787244 965 6.96×10−7 0.034 −0.55 11 644,011 — — Intergenic Island Weak transcribed
 cg07261978 950 9.52×10−7 0.038 −2.91 8 82,043,566 — — Intergenic Open Sea Weak enhancer
 cg19029576 954 1.01×10−6 0.040 −1.84 9 140,330,686 ENTPD8 Plays a central role in concentration of extracellular nucleotides. Body Island Weak transcribed
 cg25629796 971 1.12×10−6 0.041 0.35 17 11,940,467 MAP2K4 Member of the mitogen-activated protein kinase (MAPK) family, which is involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation, and development. Body Open Sea Weak transcribed
 cg01430385 954 1.20×10−6 0.042 −1.43 10 1,033,349 GTPBP4 Involved in the biogenesis of the 60S ribosomal subunit. Promoter N. Shore Active promoter
 cg02519806 948 1.50×10−6 0.045 −0.26 4 119,810,036 SYNPO2 Has an actin-binding and actin-bundling activity. Involved in regulation of cell migration; may be a tumor suppressor. Promoter Open Sea Poised promoter
 cg04915788 959 1.53×10−6 0.044 −1.04 12 25,156,888 — — Intergenic Open Sea Weak enhancer
 cg13170005 957 1.75×10−6 0.048 −4.77 17 4,690,632 VMO1 Unknown function, homolog of a gene that encodes component of the outer membrane of the vitelline layer of the egg in chickens. Promoter N. Shore Repressed
 cg26483235 938 2.16×10−6 0.050 −1.20 8 62,870,065 — — Intergenic Open Sea Heterochromatin
 cg07318309 913 2.29×10−6 0.051 0.19 5 156,537,633 HAVCR2 Cell surface receptor implicated in modulating innate and adaptive immune responses Promoter Open Sea Weak enhancer
 cg07509511 913 2.45×10−6 0.051 −1.74 2 65,297,852 CEP68 Involved in maintenance of centrosome cohesion Body Open Sea Transcription elongation
 cg11062848 913 2.57×10−6 0.052 2.08 6 13,616,537 NOL7 Maintains nucleolar structure and cell growth rates; also functions as a tumor suppressor and regulator of angiogenesis. Expression regulated by the RB tumor suppressor gene. Body S. Shore Active promoter
 cg18722557 917 2.80×10−6 0.054 0.23 10 123,734,694 NSMCE4A Component of a complex involved in DNA double-strand breaks by homologous recombination. Required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines. Promoter Island Active promoter
 cg20531550 923 2.81×10−6 0.054 −3.11 7 128,550,902 KCP Enhances bone morphogenetic protein (BMP) signaling in a paracrine manner. Promoter Island Weak transcribed
 cg05730283 933 2.96×10−6 0.055 0.42 2 62,422,808 B3GNT2 Probably constitutes the main polylactosamine synthase Promoter Island Active promoter
 cg20540608 901 2.97×10−6 0.053 1.53 5 60,241,003 NDUFAF2; ERCC8 NDUFAF2: Acts as a molecular chaperone for mitochondrial complex I assembly. ERCC8: Plays a role in DNA single-strand and double-strand breaks (DSSBs) repair; involved in repair of DSSBs by nonhomologous end joining (NHEJ) Promoter Island Active promoter
 cg25597976 929 3.00×10−6 0.055 1.05 8 74,750,772 UBE2W Promotes the ubiquitination of Fanconi anemia complementation group proteins and may be important in the repair of DNA damage Body Open Sea Weak enhancer
AMPA
 cg22171277 938 1.25×10−7 0.038 0.32 2 70,363,119 — — Intergenic Open Sea Strong enhancer
 cg23261070 946 1.55×10−7 0.041 0.13 17 6,918,037 C17orf49 Component of chromatin complexes such as the MLL1/MLL and NURF complexes Promoter Island Active promoter

Note: Linear models adjusted for urinary creatinine, age, race/ethnicity, BMI, smoking status, alcohol consumption, self-reported organic eating habits, diet quality (HEI), estimated WBC type proportions, batch, and position on chip, were fitted for all probes on the Illumina HumanMethylationEPIC array which remained after quality filtering. Results were pooled from 1,000 random subsamples of the training set (individuals per subsample). Probes that were statistically significant with FDR q<0.1 in 90% or more subsamples were considered differentially methylated. Missing data for covariates (from n=18 individuals in the training set) were substituted with the median (numeric variables) or mode (categorical variables). Chromatin state is predicted by ChromHMM from ENCODE data for the GM12878 cell line. Gene summaries are condensed from the RefSeq and UniProt gene summaries and provide a broad overview of the known function(s) of the gene product. —, no data; AMPA, aminomethylphosphonic acid; BMI, body mass index; Chr, Chromosome; FDR, false discovery rate; Freq., number of iterations in which DMP was identified as significant; HEI, Healthy Eating Index; WBC, white blood cell.