3-methylxanthine to 7-methylxanthine

Numerator Metabolite

Structure of 3-methylxanthine
Metabolite Accession: GCST90199699
Name: 3-methylxanthine
Hmdb Id: HMDB0001886
Super Pathway: NA
Sub Pathway: NA
Inchikey: GMSNIKWWOQHZGF

Denominator Metabolite

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

Associated Genomic Regions

Region: rs2472297

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

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
15
Beta (Ratio):
-0.080
Position:
75027880
SE (Ratio):
0.009
Effect Allele:
T
Z-score (Ratio):
-8.672
Reference Allele:
C
-log10(P):
-40.004
MAF:
0.250
Beta (Num):
0.031
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
0.111
SE (Den):
0.018
No CNV overlap
rQTL cluster:
216
Reaction Distance:
NA
Closest Genes:
CYP1A1 CYP1A2 EDC3 CSK LMAN1L

Region: rs56113850

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

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
19
Beta (Ratio):
-0.117
Position:
41353107
SE (Ratio):
0.008
Effect Allele:
T
Z-score (Ratio):
-14.511
Reference Allele:
C
-log10(P):
-108.185
MAF:
0.423
Beta (Num):
-0.103
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.014
SE (Den):
0.016
No CNV overlap
rQTL cluster:
244
Reaction Distance:
NA
Closest Genes:
CTC-490E21.12 CYP2A6 CYP2A7 EGLN2 RAB4B-EGLN2

LLM Analysis

Numerator Metabolite Explanation:

Caffeine Metabolism

Denominator Metabolite Explanation:

Caffeine Metabolism

Ratio Explanation:

The ratio of 3-methylxanthine to 7-methylxanthine reflects the activity of different caffeine metabolism pathways, influenced by enzymes like CYP1A2 and CYP2A6.3[1], 5[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Reduced CYP1A2 activity, indicated by an altered 3-methylxanthine/7-methylxanthine ratio, is associated with an increased risk of lung cancer and chronic kidney disease in some populations.6[1], 7[2], 8[3]

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