1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to lignoceroyl sphingomyelin (d18:1/24:0)

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 lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Associated Genomic Regions

Region: rs102275

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.336
Position:
61557803
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
19.946
Reference Allele:
T
-log10(P):
-202.148
MAF:
0.347
Beta (Num):
0.271
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.065
SE (Den):
0.016
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs12928099

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Clumped rQTL variant

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SNP Summary

Chr:
16
Beta (Ratio):
-0.148
Position:
15150505
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-8.349
Reference Allele:
C
-log10(P):
-37.217
MAF:
0.291
Beta (Num):
-0.097
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
0.052
SE (Den):
0.016
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

Region: rs7412

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.236
Position:
45412079
SE (Ratio):
0.029
Effect Allele:
T
Z-score (Ratio):
8.097
Reference Allele:
C
-log10(P):
-35.113
MAF:
0.083
Beta (Num):
0.080
Novel Locus:
Yes ✔️
SE (Num):
0.027
Beta (Den):
-0.156
SE (Den):
0.027
No CNV overlap
rQTL cluster:
8
Reaction Distance:
NA
Closest Genes:
APOE TOMM40 APOC1 PVRL2 APOC4

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism; Phosphatidylcholine biosynthesis.7[1], 8[2], 9[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism; Ceramide biosynthesis.10[1], 11[2], 12[3]

Ratio Explanation:

This ratio indicates the balance between glycerophospholipid and sphingolipid pools, likely reflecting altered lipoprotein composition and lipid homeostasis due to APOE-mediated transport.13[1], 14[2], 15[3], 16[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

APOE variants alter lipoprotein metabolism, reflected in the PC/SM ratio.13[1], 14[2] This systemic dyslipidemia is a primary causal factor for the associated phenotypes of coronary atherosclerosis and myocardial infarction by affecting lipid transport and clearance.17[3], 18[4], 19[5]

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