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

Numerator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Denominator 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

Associated Genomic Regions

Region: rs174536

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.288
Position:
61551927
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
-16.952
Reference Allele:
A
-log10(P):
-146.751
MAF:
0.341
Beta (Num):
-0.066
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.222
SE (Den):
0.016
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs12928099

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Clumped rQTL variant

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SNP Summary

Chr:
16
Beta (Ratio):
0.142
Position:
15150505
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
8.003
Reference Allele:
C
-log10(P):
-34.346
MAF:
0.291
Beta (Num):
0.052
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.091
SE (Den):
0.016
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

Region: rs7412

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.245
Position:
45412079
SE (Ratio):
0.029
Effect Allele:
T
Z-score (Ratio):
-8.394
Reference Allele:
C
-log10(P):
-37.595
MAF:
0.084
Beta (Num):
-0.156
Novel Locus:
Yes ✔️
SE (Num):
0.027
Beta (Den):
0.088
SE (Den):
0.027
No CNV overlap
rQTL cluster:
8
Reaction Distance:
NA
Closest Genes:
APOE TOMM40 APOC1 PVRL2 APOC4

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism, Phosphatidylcholine biosynthesis.5[1], 6[2]

Ratio Explanation:

The ratio reflects the balance between sphingolipid and glycerophospholipid pools. FADS1 variants alter fatty acid composition, affecting both lipid classes and cardiovascular risk.7[1], 8[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

FADS1 variants are associated with altered polyunsaturated fatty acid metabolism, which impacts the composition of membrane lipids like sphingomyelin and phosphatidylcholine, contributing to dyslipidemia and increasing the risk for cholelithiasis and cardiovascular diseases.9[1], 10[2]

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