Table 2

Association results for all 33 fatty acid phenotypes at common SNPs in the Illumina MEGA genomewide scan, in descending maternal test significance

FAGenen (SNPs)Lead SNPChrPositionRefAAltARAFβSE βDirMother P valueInfant P value
PUFA6/PUFA3*SNX291/1rs71985951612564907ag0.07−4.600.69−−4.5×10−115.1×10−6
EICIntergenic1/1rs344406282222523887ag0.090.641.08++1.2×10−109.1×10−7
AAFADS124/25rs1745561161580635tc0.170.851.03−−1.5×10−104.7×10−10
CAPCOG38/8rs12583793§1346057286ag0.060.411.15−−2.0×10−105.4×10−6
LAUSFXN50/1rs11695051273234432tc0.941.841.11++4.4×10−91.1×10−5
OLEZNF804B0/4rs12535041788573471ac0.931.191.03++5.0×10−94.5×10−6
DPA6DIAPH30/1rs760659461360373704at0.930.691.07−−5.2×10−94.9×10−7
PALATP8A20/1rs73353381326242505at0.901.131.02++2.1×10−81.8×10−6
CAPIntergenic0/4rs69869218138865556ag0.120.601.10−−2.4×10−83.7×10−6
MUFAZNF804B0/4rs12535041788573471ac0.931.181.03++4.9×10−83.2×10−5
  • SNPs shown are those with: MAF>0.05 (SNP present in both studies) or MAF>0.1 (present in only one study); info=1 in both studies and P value (HW) in infants >0.00001, with P value (association) <5×10−8, ranked by descending maternal test significance. RefA is the reference allele and AltA, the alternative allele. β and SE β are the exponentiated values from the log (FA fraction) model in mothers with the exception of the PUFA6/PUFA3. For all phenotypes except PUFA6/PUFA3, β measures the multiplicative change in the fractional composition of the FA per reference allele. All SNPs with annotated genes lie within the gene locus. n (SNPs) is the total number of SNPs significant at 4.2×10−9/5×10−8 at each locus. Sample size for all tests was 532 (PROVIDE)+610 (CRYPTO)=1142. Those results shown in bold are significant at the genomewide experiment-wise significance threshold of 4.2×10−9.

  • Individual FA abbreviations are also shown in table 1.

  • *PUFA6/PUFA3 was modelled as √(PUFA6/PUFA3), hence β is change in the ratio per allele at a standardised PUFA6/PUFA3=12.

  • †Twenty-four SNPs were significant at the experiment-wise threshold for AA, but only the top SNP is shown in this table.

  • ‡All eight CAP SNPs were in perfect LD; the listed SNP lies within H3K27Ac/H3K4Me1 marks.

  • §From the GTEx portal, rs12583793 is a cis-eQTL for: COG3 and SLC25A30 transcripts in transformed fibroblast cells, COG3 transcript in tibial artery and FAM194B (renamed ERICH6B) transcript in subcutaneous adipose tissue.

  • AA, arachidonic acid; CAP, capric acid; COG3, component of oligomeric Golgi complex 3; CRYPTO, Cryptosporidiosis in Bangladesh; DPA6, docosapentaenoic-n6; EIC, eicosenoic; FA, fatty acid; GTex, Gene–Tissue Expression Project; LAU, lauric acid; MAF, minor allele frequency; MUFA, monounsaturated fatty acid; OLE, oleic acid; PAL, palmitic acid; PROVIDE, Performance of Rotavirus and Oral Polio Vaccines in Developing Countries; RAF, Reference Allele Frequency; SNX29, sorting nexin 29.