tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*

Numerator Metabolite

Structure of tricosanoyl sphingomyelin (d18:1/23:0)*
Metabolite Accession: GCST90200034
Name: tricosanoyl sphingomyelin (d18:1/23:0)*
Hmdb Id: HMDB0012105
Super Pathway: NA
Sub Pathway: NA
Inchikey: SXZWBNWTCVLZJN

Denominator Metabolite

Metabolite Accession: GCST90200013
Name: sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs174536

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.128
Position:
61551927
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
-8.099
Reference Allele:
A
-log10(P):
-35.126
MAF:
0.341
Beta (Num):
-0.049
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.079
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs686548

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:
20
Beta (Ratio):
-0.169
Position:
12973521
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-10.989
Reference Allele:
T
-log10(P):
-63.009
MAF:
0.386
Beta (Num):
-0.049
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.120
SE (Den):
0.014
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid synthesis/metabolism.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid synthesis/metabolism.5[1], 6[2]

Ratio Explanation:

The ratio reflects fatty acid desaturase (FADS1/2) activity, indicating a shift in the balance between saturated and polyunsaturated fatty acid incorporation into sphingomyelins.2[1], 4[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

FADS1/FADS2 variants alter desaturase activity, changing the composition of sphingolipids.2[1], 4[2], 7[3] This dysregulation of lipid metabolism, including sphingomyelins, is a risk factor for cholelithiasis (gallstones), a phenotype significantly associated with these genetic and metabolic changes.8[4], 9[5], 10[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