1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to tricosanoyl sphingomyelin (d18:1/23:0)*

Numerator Metabolite

Structure of 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Metabolite Accession: GCST90200330
Name: 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Hmdb Id: HMDB0007973
Super Pathway: NA
Sub Pathway: NA
Inchikey: JLPULHDHAOZNQI

Denominator 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

Associated Genomic Regions

Region: rs102275

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.322
Position:
61557803
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
20.003
Reference Allele:
T
-log10(P):
-203.286
MAF:
0.347
Beta (Num):
0.271
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.051
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs12928099

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:
16
Beta (Ratio):
-0.140
Position:
15150505
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-8.263
Reference Allele:
C
-log10(P):
-36.494
MAF:
0.291
Beta (Num):
-0.097
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
0.044
SE (Den):
0.016
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, phospholipid biosynthesis.6[1], 7[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism, ceramide metabolism.6[1], 8[2]

Ratio Explanation:

The ratio reflects the balance of a key glycerophospholipid and a sphingomyelin, which is influenced by APOE's central role in assembling and clearing different lipoprotein particles.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variants in APOE alter lipoprotein transport and composition, which is reflected in this ratio. The resulting dyslipidemia is a known causal factor for atherosclerosis, cholelithiasis, and cardiovascular diseases such as myocardial infarction and coronary atherosclerosis.9[1], 10[2], 11[3], 12[4]

Phenotype Driver:

Gene-centric:[APOE]

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