sphingomyelin (d18:1/18:1, d18:2/18:0) to sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

Denominator Metabolite

Metabolite Accession: GCST90199995
Name: sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs102275

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.293
Position:
61557803
SE (Ratio):
0.014
Effect Allele:
C
Z-score (Ratio):
-21.349
Reference Allele:
T
-log10(P):
-231.176
MAF:
0.346
Beta (Num):
-0.114
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.179
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs680379

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.113
Position:
12969400
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-8.406
Reference Allele:
G
-log10(P):
-37.698
MAF:
0.385
Beta (Num):
-0.032
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.081
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, fatty acid biosynthesis.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism, fatty acid biosynthesis.5[1], 6[2], 7[3]

Ratio Explanation:

This ratio reflects fatty acid desaturase (FADS) activity, comparing sphingomyelins with C18 acyl chains to those with longer, more unsaturated C20/C22 chains.8[1], 9[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

FADS1 eQTL colocalization suggests altered fatty acid desaturation, modifying sphingomyelin composition.8[1], 10[2] This dyslipidemia is a key risk factor for associated phenotypes like cholelithiasis, hypercholesterolemia, and Type 2 diabetes by affecting cholesterol solubility, lipoprotein metabolism, and overall lipid homeostasis.1[3], 11[4], 12[5], 13[6]

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