FA | Gene | n (SNPs) | Lead SNP | Chr | Position | RefA | AltA | RAF | β | SE β | Dir | Mother P value | Infant P value |
PUFA6/PUFA3* | SNX29 | 1/1 | rs7198595 | 16 | 12564907 | a | g | 0.07 | −4.60 | 0.69 | −− | 4.5×10−11 | 5.1×10−6 |
EIC | Intergenic | 1/1 | rs34440628 | 2 | 222523887 | a | g | 0.09 | 0.64 | 1.08 | ++ | 1.2×10−10 | 9.1×10−7 |
AA† | FADS1 | 24/25 | rs174556 | 11 | 61580635 | t | c | 0.17 | 0.85 | 1.03 | −− | 1.5×10−10 | 4.7×10−10 |
CAP‡ | COG3 | 8/8 | rs12583793§ | 13 | 46057286 | a | g | 0.06 | 0.41 | 1.15 | −− | 2.0×10−10 | 5.4×10−6 |
LAU | SFXN5 | 0/1 | rs11695051 | 2 | 73234432 | t | c | 0.94 | 1.84 | 1.11 | ++ | 4.4×10−9 | 1.1×10−5 |
OLE | ZNF804B | 0/4 | rs12535041 | 7 | 88573471 | a | c | 0.93 | 1.19 | 1.03 | ++ | 5.0×10−9 | 4.5×10−6 |
DPA6 | DIAPH3 | 0/1 | rs76065946 | 13 | 60373704 | a | t | 0.93 | 0.69 | 1.07 | −− | 5.2×10−9 | 4.9×10−7 |
PAL | ATP8A2 | 0/1 | rs7335338 | 13 | 26242505 | a | t | 0.90 | 1.13 | 1.02 | ++ | 2.1×10−8 | 1.8×10−6 |
CAP | Intergenic | 0/4 | rs6986921 | 8 | 138865556 | a | g | 0.12 | 0.60 | 1.10 | −− | 2.4×10−8 | 3.7×10−6 |
MUFA | ZNF804B | 0/4 | rs12535041 | 7 | 88573471 | a | c | 0.93 | 1.18 | 1.03 | ++ | 4.9×10−8 | 3.2×10−5 |
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.