An atlas of genetic influences on human blood metabolites

Shin et al., Nature Genetics, 2014 [ Article | SI Text ]

Locus 88: FADS1 (11q12.2)

Meta-analysis summary statistics for associations meeting genome-wide significance
Lead SNPBiochemicalsEA/OANtotalEAFEffect (SE)PmetaDetails
rs174548 arachidonate (20:4n6) / dihomo-linolenate (20:3n3 or n6) C/G 7350 0.7 0.071 (0.002) 1.53·10-361 show
rs174535 1-arachidonoylglycerophosphocholine* T/C 7063 0.66 0.056 (0.003) 1.86·10-94 show
rs174548 arachidonate (20:4n6) C/G 7367 0.7 0.049 (0.003) 1.43·10-84 show
rs174578 1-arachidonoylglycerophosphoethanolamine* A/T 7350 0.34 -0.035 (0.003) 6.12·10-42 show
rs174535 1-linoleoylglycerophosphoethanolamine* T/C 7369 0.67 -0.044 (0.004) 2.82·10-36 show
rs174578 1-arachidonoylglycerophosphoinositol* A/T 7351 0.34 -0.027 (0.003) 3.02·10-24 show
rs174550 adrenate (22:4n6) T/C 7330 0.67 0.035 (0.003) 6.79·10-24 show
rs174556 eicosapentaenoate (EPA; 20:5n3) T/C 7367 0.3 -0.036 (0.004) 1.97·10-22 show
rs968567 dihomo-linolenate (20:3n3 or n6) T/C 7358 0.18 0.033 (0.004) 2.14·10-21 show
rs968567 1-eicosatrienoylglycerophosphocholine* T/C 7362 0.18 0.040 (0.005) 2.84·10-19 show
rs174601 stearidonate (18:4n3) T/C 7330 0.34 -0.034 (0.004) 7.93·10-16 show
rs174538 docosapentaenoate (n3 DPA; 22:5n3) A/G 7373 0.3 -0.026 (0.004) 8.9·10-14 show

EA = effect allele; OA = other allele; EAF = frequency of effect allele;

Summary of biological annotations
SNPrs174548
Chromosomal locationChr11: 61,327,924 (11q12.2)
Gene (distance)FADS1 (0)
Predicted causal geneFADS1
Gene/protein classification-
Metabolite (Pathway)arachidonate (20:4n6) (Long chain fatty acid; Lipid)
dihomo-linolenate (20:3n3 or n6) (Essential fatty acid; Lipid)
Biochemical locus-metabolite relationshipFADS1, FADS2 and FADS3 encode three homologous fatty acid desaturases; FADS1 is a delta-5 desaturase, FADS2 is a delta-6 desaturase, and the catalytic activity of FADS3 is unknown [10601301]. The ratio of arachidonate (20:4n6) to dihomo?linolenate (20:3n3 or n6) represents a product/substrate pair for FADS1. Ratio interpretation: n/a.
eQTL associationsFADS1 (H), FADS1 (F), FADS3 (H)

F = adipose tissue; S = skin cells; L = lymphoblastoid cells; H = liver cells;

Medical information
Complex trait associationsCholesterol, total [20686565]; Comprehensive strength and appendicular lean mass [22960237]; Crohn's disease [21102463]; Fasting glucose-related traits [20081858]; Fasting glucose-related traits (interaction with BMI) [22581228]; HDL cholesterol [19060906,20864672,20686565]; Hematology traits [23303382]; LDL cholesterol [19060910,20686565]; Lipid metabolism phenotypes [22286219]; Metabolic syndrome [20694148]; Response to statin therapy [20339536]; Resting heart rate [20639392]; Triglycerides [19060906,20864672,20686565]
Known metabolite associations1-arachidonoylglycerophosphoethanolamine*/1-linoleoylglycerophosphoethanolamine* [21886157]; PC aa C36:3/PC aa C36:4 [20037589]; PC aa C36:4 [19043545]; Metabolite levels [19043545,23281178,22916037]; Oleic acid (18:1n-9) plasma levels [23362303]; Palmitoleic acid (16:1n-7) plasma levels [23362303]; Phospholipid levels (plasma) [22359512,21829377]; Stearic acid (18:0) plasma levels [23362303]; PC 38:4 [23823483]
Inborn error of metabolism-

Pharmacological information
ChEMBL ID-
Drug information Compounds with activity in ChEMBL for FADS2

Locus information for top associated metabolite

HapMap2 imputation

Imputation HapMap

1KGP imputation

Imputation 1KGP

 

Network view
Association map