1-methylxanthine to paraxanthine

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 paraxanthine
Metabolite Accession: GCST90199654
Name: paraxanthine
Hmdb Id: HMDB0001860
Super Pathway: NA
Sub Pathway: NA
Inchikey: QUNWUDVFRNGTCO

Associated Genomic Regions

Region: rs56113850

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.113
Position:
41353107
SE (Ratio):
0.011
Effect Allele:
T
Z-score (Ratio):
-10.432
Reference Allele:
C
-log10(P):
-56.993
MAF:
0.424
Beta (Num):
-0.001
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.111
SE (Den):
0.016
No CNV overlap
rQTL cluster:
244
Reaction Distance:
1.0
Closest Genes:
CTC-490E21.12 CYP2A6 CYP2A7 EGLN2 RAB4B-EGLN2

Region: rs1495741

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Clumped rQTL variant

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SNP Summary

Chr:
8
Beta (Ratio):
-0.374
Position:
18272881
SE (Ratio):
0.013
Effect Allele:
G
Z-score (Ratio):
-29.331
Reference Allele:
A
-log10(P):
-433.758
MAF:
0.222
Beta (Num):
-0.366
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
0.008
SE (Den):
0.019
No CNV overlap
rQTL cluster:
85
Reaction Distance:
1.0
Closest Genes:
NAT2 PSD3 NAT1 ASAH1 PCM1

LLM Analysis

Numerator Metabolite Explanation:

Caffeine metabolism

Denominator Metabolite Explanation:

Caffeine metabolism

Ratio Explanation:

This ratio reflects the activity of enzymes metabolizing paraxanthine, a major caffeine metabolite, into 1-methylxanthine, indicating the rate of caffeine processing in the liver.3[1], 4[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants in CYP2A6 and NAT2 alter caffeine metabolism, which is linked to smoking-related cancers (lung, bladder) and cardiovascular phenotypes.5[1], 6[2], 2[3] The gene's role in metabolizing carcinogens from tobacco is a primary driver of the cancer association, with the caffeine metabolite ratio acting as a proxy for enzyme activity.

Phenotype Driver:

Gene-centric:CYP2A6

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