3-methylxanthine to indolin-2-one

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 indolin-2-one
Metabolite Accession: GCST90199944
Name: indolin-2-one
Hmdb Id: HMDB0061918
Super Pathway: NA
Sub Pathway: NA
Inchikey: JYGFTBXVXVMTGB

Associated Genomic Regions

Region: rs56113850

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:
19
Beta (Ratio):
-0.270
Position:
41353107
SE (Ratio):
0.022
Effect Allele:
T
Z-score (Ratio):
-12.304
Reference Allele:
C
-log10(P):
-78.433
MAF:
0.423
Beta (Num):
-0.103
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.167
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, Xenobiotic metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio likely reflects CYP2A6 activity, which metabolizes both 3-methylxanthine (from caffeine) and indole (the precursor of indolin-2-one).2[1], 7[2], 10[3]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in CYP2A6 alter the metabolism of nicotine and tobacco carcinogens, which directly impacts the risk for smoking-related diseases like emphysema and lung cancer.1[1], 3[2], 11[3], 12[4] Altered liver enzyme levels (ALT, ALP) are consistent with CYP2A6's primary function in the liver.13[5], 14[6]

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