choline to glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*

Numerator Metabolite

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

Denominator Metabolite

Metabolite Accession: GCST90200117
Name: glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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):
-0.199
Position:
211540507
SE (Ratio):
0.022
Effect Allele:
A
Z-score (Ratio):
-8.919
Reference Allele:
C
-log10(P):
-42.201
MAF:
0.310
Beta (Num):
-0.090
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.108
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio may reflect a shift in lipid metabolism, where altered CPS1 function impacts both choline and sphingolipid pathways, potentially influencing nitrogen and lipid homeostasis.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Altered CPS1 activity, influenced by the missense variant, may disrupt urea cycle and downstream choline and sphingolipid metabolism, contributing to cholelithiasis and renal dysfunction.7[1], 8[2], 10[3], 11[4], 12[5], 13[6]

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