1-stearoyl-2-linoleoyl-gpc (18:0/18:2)* to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

Numerator Metabolite

Structure of 1-stearoyl-2-linoleoyl-gpc (18:0/18:2)*
Metabolite Accession: GCST90200037
Name: 1-stearoyl-2-linoleoyl-gpc (18:0/18:2)*
Hmdb Id: HMDB0008039
Super Pathway: NA
Sub Pathway: NA
Inchikey: FORFDCPQKJHEBF

Denominator Metabolite

Structure of sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

Associated Genomic Regions

Region: rs102275

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.326
Position:
61557803
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
19.526
Reference Allele:
T
-log10(P):
-193.828
MAF:
0.347
Beta (Num):
0.220
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.106
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs12928099

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:
16
Beta (Ratio):
-0.152
Position:
15150505
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-8.661
Reference Allele:
C
-log10(P):
-39.901
MAF:
0.291
Beta (Num):
-0.091
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.062
SE (Den):
0.016
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

LLM Analysis

Numerator Metabolite Explanation:

Phosphatidylcholine biosynthesis

Denominator Metabolite Explanation:

Sphingomyelin and ceramide metabolism5[1], 6[2], 7[3]

Ratio Explanation:

This ratio may reflect the balance between fatty acid desaturation by FADS1 and sphingolipid synthesis, both crucial for membrane composition and signaling.5[1], 8[2], 9[3]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variations in FADS1 affect its desaturase activity, altering the abundance of specific fatty acids in phospholipids and sphingolipids.10[1], 8[2], 9[3] This impacts lipid profiles, contributing to phenotypes like hypercholesterolemia, cholelithiasis, and type 2 diabetes.3[4], 11[5], 12[6], 13[7]

Phenotype Driver:

Gene-centric:FADS1

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