sphingomyelin (d18:2/24:2)* to sphingomyelin (d18:2/23:1)*

Numerator Metabolite

Structure of sphingomyelin (d18:2/24:2)*
Metabolite Accession: GCST90200124
Name: sphingomyelin (d18:2/24:2)*
Hmdb Id: HMDB0240644
Super Pathway: NA
Sub Pathway: NA
Inchikey: LAWJSGKLPKMOGG

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: rs364585

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):
-0.088
Position:
12962718
SE (Ratio):
0.011
Effect Allele:
A
Z-score (Ratio):
-7.805
Reference Allele:
G
-log10(P):
-32.755
MAF:
0.385
Beta (Num):
-0.029
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.060
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 metabolism.3[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.3[1], 5[2]

Ratio Explanation:

This ratio reflects the balance between two specific sphingomyelin species, which is influenced by the substrate preference of the SPTLC3-containing enzyme complex.1[1], 5[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SPTLC3 activity can modify the composition of sphingolipids, which has been associated with changes in LDL-cholesterol and an increased risk for cholelithiasis, also known as gallstone disease.3[1], 6[2], 7[3], 8[4]

Phenotype Driver:

Gene-centric:SPTLC3

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