tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:2/21:0, d16:2/23:0)*

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: GCST90200129
Name: sphingomyelin (d18:2/21:0, d16:2/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.137
Position:
8289519
SE (Ratio):
0.015
Effect Allele:
C
Z-score (Ratio):
8.935
Reference Allele:
A
-log10(P):
-42.343
MAF:
0.192
Beta (Num):
0.055
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
-0.081
SE (Den):
0.016
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs4814175

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):
-0.114
Position:
12959094
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-9.141
Reference Allele:
T
-log10(P):
-44.229
MAF:
0.386
Beta (Num):
-0.048
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.066
SE (Den):
0.013
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis.4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the relative activity of ceramide synthases; CERS4 influences the synthesis of the numerator's ceramide precursor with a C23:0 fatty acid.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered CERS4 activity changes sphingolipid composition, affecting LDL-cholesterol levels and liver function (ALT).7[1], 8[2], 9[3], 10[4] Disruptions in sphingolipid metabolism are linked to cholelithiasis, potentially mediated by changes in LDL and bile composition.11[5], 12[6], 13[7]

Phenotype Driver:

Gene-centric:CERS4

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