1-methylxanthine to caffeine

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 caffeine
Metabolite Accession: GCST90200436
Name: caffeine
Hmdb Id: HMDB0001847
Super Pathway: NA
Sub Pathway: NA
Inchikey: RYYVLZVUVIJVGH

Associated Genomic Regions

Region: rs2472297

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Clumped rQTL variant

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SNP Summary

Chr:
15
Beta (Ratio):
0.171
Position:
75027880
SE (Ratio):
0.015
Effect Allele:
T
Z-score (Ratio):
11.650
Reference Allele:
C
-log10(P):
-70.552
MAF:
0.250
Beta (Num):
0.149
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.022
SE (Den):
0.018
No CNV overlap
rQTL cluster:
216
Reaction Distance:
2.0
Closest Genes:
CYP1A1 CYP1A2 EDC3 CSK LMAN1L

Region: rs1495743

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Clumped rQTL variant

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SNP Summary

Chr:
8
Beta (Ratio):
-0.370
Position:
18273300
SE (Ratio):
0.015
Effect Allele:
G
Z-score (Ratio):
-24.336
Reference Allele:
C
-log10(P):
-299.529
MAF:
0.223
Beta (Num):
-0.368
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.002
SE (Den):
0.019
No CNV overlap
rQTL cluster:
85
Reaction Distance:
2.0
Closest Genes:
NAT2 PSD3 NAT1 ASAH1 PCM1

LLM Analysis

Numerator Metabolite Explanation:

Caffeine metabolism

Denominator Metabolite Explanation:

Caffeine metabolism

Ratio Explanation:

This ratio indicates the rate of caffeine clearance.3[1] A higher ratio suggests faster metabolism of caffeine into its downstream product, 1-methylxanthine.4[2], 5[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Variations in CYP1A2 and NAT2 genes alter caffeine metabolism rates, influencing the risk for malignant neoplasm of the bladder, particularly in smokers.6[1], 7[2] Slower metabolism (lower ratio) is associated with increased risk.6[3], 7[4], 8[5]

Phenotype Driver:

Gene-centric:CYP1A2

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