Table 3. Functional annotations of novel loci and associated SNPs (details on eQTLs and ENCODE annotations in Supplementary Tables 14 and 15, Supplementary Data 2 and 3)16,21,22,23,24,25,37,38,39,40,41,42,43.

SNP/locus	eQTL/ENCODE	Other diseases	Known functions of genes
rs207403811p11.2SNP location: Lies within either the first intron or 5′ UTR of the various ACCS/PHACS gene isoformsWithin the same LD block as the adjacent gene EXT2.	Risk allele is strongly associated with increased ACCS gene expression levels in peripheral blood cells (P<9.81 × 10−198), monocytes (P=1.07 × 10−36), and B-cells (P=1.46 × 10−29).It is also associated with increased EXT2 expression levels in peripheral blood cells (P=2.63 × 10−53).This SNP and others in LD are also located at sites predicted with high likelihood to affect chromatin structure and protein binding.	Not previously associated with any other trait.	ACCS encodes a1-aminocyclopropane-1-carboxylate synthase homologue that belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.Shown to interact with the protein encoded by FBF1 (Fas (TNFRSF6) binding factor 1), a keratin-binding protein that is required for epithelial cell polarization, apical junction complex assembly andciliogenesis37,38EXT2 is a glycosyltransferase, which plays a role in heparan sulfate biosynthesis. Heparan sulfate in turn influences angiogenesis and cell proliferation; mutations in this gene cause multiple exotoses39,40.
rs76343893q27.3SNP location: Lies within an intron of the ST6GAL1.	Risk allele is in strong LD (r2>0.9 in our samples, HapMap Europeans and Asians) with variants associated with decreased expression levels of ST6GAL1 in peripheral blood cells (rs3821819; P=5.96 × 10−20) and B-cells (rs17776120; P=1.61 × 10−7).This SNP and others in LD may affect chromatin structure and protein binding.	IgG glycosylation, Type 2 diabetes, oesophageal cancer.Drug-induced liver injury.In moderate LD with rs11710456 in IgG glycosylation in Europeans (r2=0.528) but not Asians (r2=0.12).	ST6GAL1 encodes ST6 beta-galactosamide alpha-2,6-sialyltranferase, a member of glycosyltransferase family involved in the generation of the cell-surface carbohydrate determinants and differentiation antigens.Regulates macrophage apoptosis via alpha2-6 sialylation of the TNFR1 death receptor.May play a regulatory role in innate immune response.Up-regulated in human cancers41,42.
rs20335628q22.3SNP location: Located in an intergenic region closest to the genes ODF1, KLF10 and UBR5.	No evidence for effects on gene expression levels in peripheral blood cells, monocytes, B-cells.In LD with SNPs with potential regulatory effects on UBR5 expression, chromatin structure and protein binding.	Chronic lymphocytic leukaemia (CLL)Not in LD with CLL-associated SNP.	KLF10 encodes a transcriptional repressor that acts as an effector of transforming growth factor beta signalling and activity of this protein may inhibit the growth of cancers.UBR5 encodes a E3 ubiquitin ligase which interacts with the deubiquitinase DUBA which in turns plays a role in IL-17 production in T-cells and inflammatory response in the small intestine43.

SNP, single-nucleotide polymorphism.

Other recently and previously reported loci are described in Supplementary Table 13.