7-methylxanthine to theobromine

Numerator Metabolite

Structure of 7-methylxanthine
Metabolite Accession: GCST90199754
Name: 7-methylxanthine
Hmdb Id: HMDB0001991
Super Pathway: NA
Sub Pathway: NA
Inchikey: PFWLFWPASULGAN

Denominator Metabolite

Structure of theobromine
Metabolite Accession: GCST90199644
Name: theobromine
Hmdb Id: HMDB0002825
Super Pathway: NA
Sub Pathway: NA
Inchikey: YAPQBXQYLJRXSA

Associated Genomic Regions

Region: rs2472297

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Clumped rQTL variant

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SNP Summary

Chr:
15
Beta (Ratio):
0.138
Position:
75027880
SE (Ratio):
0.012
Effect Allele:
T
Z-score (Ratio):
11.616
Reference Allele:
C
-log10(P):
-70.152
MAF:
0.250
Beta (Num):
0.111
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
-0.027
SE (Den):
0.018
No CNV overlap
rQTL cluster:
216
Reaction Distance:
3.0
Closest Genes:
CYP1A1 CYP1A2 EDC3 CSK LMAN1L

Region: rs56113850

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.092
Position:
41353107
SE (Ratio):
0.010
Effect Allele:
T
Z-score (Ratio):
-8.856
Reference Allele:
C
-log10(P):
-41.632
MAF:
0.424
Beta (Num):
0.014
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.106
SE (Den):
0.016
No CNV overlap
rQTL cluster:
244
Reaction Distance:
3.0
Closest Genes:
CTC-490E21.12 CYP2A6 CYP2A7 EGLN2 RAB4B-EGLN2

Region: rs4410790

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
7
Beta (Ratio):
-0.090
Position:
17284577
SE (Ratio):
0.011
Effect Allele:
T
Z-score (Ratio):
-8.423
Reference Allele:
C
-log10(P):
-37.844
MAF:
0.373
Beta (Num):
-0.061
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.030
SE (Den):
0.016
No CNV overlap
rQTL cluster:
233
Reaction Distance:
3.0
Closest Genes:
AHR AGR3 AGR2 AC073333.1 TSPAN13

LLM Analysis

Numerator Metabolite Explanation:

Caffeine Metabolism

Denominator Metabolite Explanation:

Caffeine Metabolism

Ratio Explanation:

The ratio of 7-methylxanthine to theobromine, both caffeine metabolites, reflects the activity of caffeine-metabolizing enzymes like CYP1A2 and CYP2A6.8[1], 1[2], 9[3], 10[4]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants in CYP1A2 and CYP2A6 alter enzyme activity, impacting the 7-methylxanthine/theobromine ratio.1[1], 10[2], 11[3], 12[4] This altered capacity to metabolize xenobiotics, including those in tobacco smoke, is the established causal link to the increased risk of lung cancer and emphysema.4[5], 5[6], 13[7], 14[8], 6[9]

Phenotype Driver:

Gene-centric:CYP1A2/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