choline to n-acetylputrescine

Numerator Metabolite

Structure of choline
Metabolite Accession: GCST90200327
Name: choline
Hmdb Id: HMDB0000097
Super Pathway: NA
Sub Pathway: NA
Inchikey: CRBHXDCYXIISFC

Denominator Metabolite

Structure of n-acetylputrescine
Metabolite Accession: GCST90200351
Name: n-acetylputrescine
Hmdb Id: HMDB0002064
Super Pathway: NA
Sub Pathway: NA
Inchikey: KLZGKIDSEJWEDW

Associated Genomic Regions

Region: rs1047891

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:
2
Beta (Ratio):
-0.161
Position:
211540507
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
-8.116
Reference Allele:
C
-log10(P):
-35.267
MAF:
0.310
Beta (Num):
-0.090
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.071
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
5.0
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Phospholipid synthesis, one-carbon metabolism, acetylcholine synthesis.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Polyamine metabolism, GABA biosynthesis.8[1], 9[2], 10[3]

Ratio Explanation:

The ratio may reflect altered nitrogen metabolism due to CPS1 dysfunction, with unclear direct biochemical linkage between choline and N-acetylputrescine metabolism.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Reduced CPS1 function can cause hyperammonemia, leading to renal stress and failure.11[1], 12[2], 13[3] Choline's role in lipid transport and CPS1's presence in bile might link their disruption to cholelithiasis, a condition associated with CPS1 variants.14[4], 15[5], 16[6], 17[7]

Phenotype Driver:

Gene-centric:CPS1

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