1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

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 sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

Associated Genomic Regions

Region: rs102275

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.377
Position:
61557803
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
21.792
Reference Allele:
T
-log10(P):
-240.757
MAF:
0.347
Beta (Num):
0.271
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.106
SE (Den):
0.015
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):
-0.158
Position:
15150505
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-8.663
Reference Allele:
C
-log10(P):
-39.921
MAF:
0.291
Beta (Num):
-0.097
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
0.062
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 biosynthesis1[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism7[1]

Ratio Explanation:

The ratio reflects the balance between glycerophospholipid and sphingolipid synthesis, influenced by FADS1/FADS2 activity which provides polyunsaturated fatty acids for both pathways.1[1], 2[2], 8[3], 7[4], 9[5]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Variations in FADS1/FADS2 genes affect the balance of fatty acids incorporated into glycerophospholipids and sphingolipids. This altered lipid profile is associated with an increased risk for inflammatory conditions and metabolic diseases like cholelithiasis, pure hypercholesterolemia, and Type 2 diabetes.10[1], 11[2]

Phenotype Driver:

Gene-centric:FADS1/FADS2

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