1-methylxanthine to 5-acetylamino-6-formylamino-3-methyluracil

Numerator Metabolite

Structure of 1-methylxanthine
Metabolite Accession: GCST90199763
Name: 1-methylxanthine
Hmdb Id: HMDB0010738
Super Pathway: NA
Sub Pathway: NA
Inchikey: MVOYJPOZRLFTCP

Denominator Metabolite

Structure of 5-acetylamino-6-formylamino-3-methyluracil
Metabolite Accession: GCST90200680
Name: 5-acetylamino-6-formylamino-3-methyluracil
Hmdb Id: HMDB0011105
Super Pathway: NA
Sub Pathway: NA
Inchikey: RDZNZFGKEVDNPK

Associated Genomic Regions

Region: rs17692943

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Clumped rQTL variant

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SNP Summary

Chr:
8
Beta (Ratio):
0.202
Position:
18029020
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
11.343
Reference Allele:
T
-log10(P):
-66.994
MAF:
0.369
Beta (Num):
0.065
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.136
SE (Den):
0.017
No CNV overlap
rQTL cluster:
221
Reaction Distance:
NA
Closest Genes:
NAT1 ASAH1 PCM1 NAT2 FGL1

Region: rs13266992

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Clumped rQTL variant

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SNP Summary

Chr:
8
Beta (Ratio):
-0.886
Position:
18239697
SE (Ratio):
0.022
Effect Allele:
C
Z-score (Ratio):
-40.858
Reference Allele:
T
-log10(P):
-838.633
MAF:
0.172
Beta (Num):
-0.256
Novel Locus:
No
SE (Num):
0.021
Beta (Den):
0.629
SE (Den):
0.020
No CNV overlap
rQTL cluster:
85
Reaction Distance:
NA
Closest Genes:
NAT2 PSD3 NAT1 ASAH1 PCM1

LLM Analysis

Numerator Metabolite Explanation:

Caffeine metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Caffeine metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

The ratio of 1-methylxanthine to AFMU, both caffeine metabolites, is a known indicator of NAT2 enzyme activity, distinguishing between rapid and slow acetylators.10[1], 11[2], 12[3], 13[4]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

NAT2 slow acetylator status, indicated by the caffeine metabolite ratio, is associated with an increased risk for bladder cancer due to altered metabolism of carcinogens.14[1], 15[2], 16[3] Additionally, NAT2 variants are linked to changes in lipid levels, connecting to lipoprotein metabolism disorders.17[4], 18[5], 19[6]

Phenotype Driver:

Gene-centric:NAT2

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data