sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/18:1, d18:2/18:0)

Numerator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator 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

Associated Genomic Regions

Region: rs9420792

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
10
Beta (Ratio):
0.127
Position:
102258439
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
7.586
Reference Allele:
C
-log10(P):
-31.045
MAF:
0.220
Beta (Num):
0.060
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
-0.067
SE (Den):
0.017
No CNV overlap
rQTL cluster:
269
Reaction Distance:
NA
Closest Genes:
SEC31B NDUFB8 NDUFB8 WNT8B HIF1AN

Region: rs1466448

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
19
Beta (Ratio):
0.279
Position:
8289519
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
15.983
Reference Allele:
A
-log10(P):
-130.725
MAF:
0.192
Beta (Num):
0.075
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.204
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid de novo biosynthesis4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid de novo biosynthesis4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects CERS4 activity, which modulates the balance of long-chain (denominator) versus very-long-chain (numerator) sphingomyelins, precursors of which are ceramides.2[1], 3[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Altered CERS4 activity, supported by eQTL data, likely modifies sphingomyelin acyl chain composition.7[1] This dysregulation of sphingolipid metabolism is associated with type 2 diabetes, potentially through impaired pancreatic β-cell function, and may also influence height and alkaline phosphatase levels. 8[2], 9[3], 10[4], 11[5], 12[6]

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