sphingomyelin (d18:1/18:1, d18:2/18:0) to sphingomyelin (d18:2/23:1)*

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

Structure of sphingomyelin (d18:2/23:1)*
Metabolite Accession: GCST90200126
Name: sphingomyelin (d18:2/23:1)*
Hmdb Id: HMDB0240668
Super Pathway: NA
Sub Pathway: NA
Inchikey: PUTLJICFLAOKRD

Associated Genomic Regions

Region: rs603424

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
0.130
Position:
102075479
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
7.664
Reference Allele:
G
-log10(P):
-31.651
MAF:
0.176
Beta (Num):
0.078
Novel Locus:
Yes ✔️
SE (Num):
0.019
Beta (Den):
-0.052
SE (Den):
0.018
No CNV overlap
rQTL cluster:
67
Reaction Distance:
NA
Closest Genes:
PKD2L1 BLOC1S2 SCD CWF19L1 CHUK

Region: rs1466448

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:
19
Beta (Ratio):
-0.262
Position:
8289519
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
-16.107
Reference Allele:
A
-log10(P):
-132.731
MAF:
0.191
Beta (Num):
-0.204
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
0.058
SE (Den):
0.017
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

LLM Analysis

Numerator Metabolite Explanation:

Sphingomyelin de novo biosynthesis

Denominator Metabolite Explanation:

Sphingomyelin de novo biosynthesis

Ratio Explanation:

This ratio reflects ceramide synthase 4 (CERS4) activity.4[1] CERS4 preferentially synthesizes precursors for the numerator (C18 chains) over the denominator (C23 chain).1[2], 4[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered CERS4 activity changes the balance of sphingomyelin species.4[1] This dysregulation of sphingolipid metabolism is associated with an increased risk of coronary atherosclerosis and hypercholesterolemia.5[2], 6[3], 7[4]

Phenotype Driver:

Metabolite-centric[both]

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