choline to isovalerylglycine

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 isovalerylglycine
Metabolite Accession: GCST90199785
Name: isovalerylglycine
Hmdb Id: HMDB00678
Super Pathway: NA
Sub Pathway: NA
Inchikey: ZRQXMKMBBMNNQC

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):
-0.310
Position:
211540507
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
-13.514
Reference Allele:
C
-log10(P):
-94.150
MAF:
0.310
Beta (Num):
-0.090
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.219
SE (Den):
0.018
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Phosphatidylcholine biosynthesis, one-carbon metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Leucine catabolism, fatty acid metabolism.7[1], 8[2], 9[3], 10[4]

Ratio Explanation:

The ratio reflects a potential disruption in nitrogen disposal and amino acid breakdown, as CPS1 deficiency impacts urea cycle function.1[1], 3[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CPS1 gene variants can impair the urea cycle, leading to nitrogen accumulation.3[1] This disruption, along with altered choline and isovalerylglycine metabolism, is associated with an increased risk for cholelithiasis and chronic kidney disease.11[2], 12[3]

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