5-acetylamino-6-amino-3-methyluracil to caffeine

Numerator Metabolite

Structure of 5-acetylamino-6-amino-3-methyluracil
Metabolite Accession: GCST90199760
Name: 5-acetylamino-6-amino-3-methyluracil
Hmdb Id: HMDB0004400
Super Pathway: NA
Sub Pathway: NA
Inchikey: POQOTWQIYYNXAT

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):
0.144
Position:
75027880
SE (Ratio):
0.016
Effect Allele:
T
Z-score (Ratio):
9.154
Reference Allele:
C
-log10(P):
-44.353
MAF:
0.251
Beta (Num):
0.121
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.022
SE (Den):
0.018
No CNV overlap
rQTL cluster:
216
Reaction Distance:
NA
Closest Genes:
CYP1A1 CYP1A2 EDC3 CSK LMAN1L

Region: rs1495741

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:
8
Beta (Ratio):
0.383
Position:
18272881
SE (Ratio):
0.016
Effect Allele:
G
Z-score (Ratio):
23.759
Reference Allele:
A
-log10(P):
-285.650
MAF:
0.226
Beta (Num):
0.384
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
6.34e-04
SE (Den):
0.019
No CNV overlap
rQTL cluster:
85
Reaction Distance:
NA
Closest Genes:
NAT2 PSD3 NAT1 ASAH1 PCM1

LLM Analysis

Numerator Metabolite Explanation:

Caffeine metabolism.12[1], 13[2], 14[3], 15[4]

Denominator Metabolite Explanation:

Caffeine metabolism.16[1], 17[2], 18[3], 19[4], 20[5], 21[6], 4[7], 22[8], 12[9]

Ratio Explanation:

This ratio reflects the activity of N-acetyltransferase 2 (NAT2), where a lower ratio indicates faster acetylation of caffeine metabolites.13[1], 11[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in NAT2 determines acetylator status (slow vs. fast), which alters caffeine metabolism.2[1], 3[2], 23[3], 5[4] Slow acetylator status is associated with an increased risk for malignant neoplasm of the bladder.24[5], 9[6], 10[7], 11[8]

Phenotype Driver:

Gene-centric:NAT2

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