Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.(Extended Data Fig. 5). These results show the value of large sample sizes in blood to detect trans-mQTLs regardless of the tissue. Trans-mQTL SNPs and DNAm exhibit patterned TF binding.Recent studies have uncovered multiple types of transcription factor (TF)-DNA interactions influenced by DNAm, including the binding of DNAm-sensitive TFs [26][27][28] and cooperativity between TFs 27,29 . To gain insights into how SNPs induce long-range DNAm changes, we mapped enrichments for DNAm sites and SNPs across binding sites for 171 TFs in 27 cell types 30,31 . We found strong enrichments for most TFs and cell types among DNAm sites with a trans association (cis + trans: 55%; trans only: 80%; cis only: 18%) and among cis-acting SNPs (cis only: 96%, cis + trans: 91%, trans only: 1%; Fig. 2b, Supplementary Tables 7 and 8, and Supplementary Figs. 22 and 23). Consistent with the observation that trans-only DNAm sites are enriched for CpG islands (Supplementary Fig. 13), DNAm sites that overlap TF-binding sites (TFBSs) were relatively hypomethylated (weighted mean DNAm levels = 21% versus 52%, P < 2.2 × 10 −16 ; Supplementary Fig. 24).Next, we hypothesized that, if a trans-mQTL is driven by TF activity 8,10 , then particular TF-TF pairs may exhibit preferential enrichment 32 . An mQTL has a pair of TFBS annotations 31 , one for the SNP and one for the DNAm site. We evaluated whether the annotation pairs among 18,584 interchromosomal trans-mQTLs were associated with TF binding in a nonrandom pattern (Supplementary Note and Extended Data Fig. 6a,b). We found that 6.1% (22,962 of 378,225) of possible pairwise combinations of SNP-DNAm site annotations were more over-or underrepresented than expected by chance after strict multiple testing correction (Supplementary Note, Supplementary Table 9 and Extended Data Fig. 6c).After accounting for abundance and other characteristics, the strongest pairwise enrichments involved sites close to TFBSs for proteins in the cohesin complex, ...

We evaluated the roles of five single-nucleotide polymorphisms (SNPs) within PDCD1, and haplotypes defined by these SNPs, for the development of systemic lupus erythematosus (SLE) and specific sub-phenotypes (nephritis, antiphospholipid antibody positive, arthritis and double-stranded DNA positive) within a multiethnic US cohort of 1036 patients. Family based analyses were performed using 844 simplex families from four ethnic groups (Caucasian, Asian, Hispanic and African American). Subjects were genotyped for five 'tag' SNPs (selected from 15) to provide complete genetic information in all main ethnic groups. We employed transmission disequilibrium testing to assess risk for SLE by allele or haplotype, and multiple logistic regression analysis of SLE cases to examine associations with specific sub-phenotypes. In family based analyses, a haplotype containing the PD1.3A allele was significantly associated with SLE susceptibility among Caucasian families (P ¼ 0.01). Among Hispanic families, two novel SNPs were associated with SLE risk (P ¼ 0.005 and 0.01). In multivariate logistic regression analyses, five haplotypes were associated with specific sub-phenotypes among the different ethnic groups. These results suggest that PDCD1 genetic variation influences the risk and expression of SLE and that these associations vary according to ethnic background.

The aim of this study was to analyze in families with SLE for the presence of linkage and the structure and transmission of haplotypes containing alleles for the low-affinity Fcg receptors. The Fcg receptor polymorphisms FcgRIIA-131R/H, FcgRIIIA-176F/V and FcgRIIIB-NA1/2 and a polymorphism in the FcgRIIB gene were genotyped with RFLP, allele-specific PCR or pyrosequencing. Individual SNPs and haplotypes were tested for linkage in multicase families and for association using contingency tables, transmission disequilibrium test and affected family-based control groups in Swedish and Mexican singlecase families. No linkage or association could be detected using the FcgR polymorphisms in the multicase families. However, an association was found for both FcgRIIA-131R and IIIA-176F alleles in the single-case families, but not for IIIB or IIB. Allelic association to SLE was found for a haplotype that included both risk alleles, but not in haplotypes where only one or the other was present. We propose that FcgRIIA-131R and FcgRIIIA-176F are both risk alleles for SLE transmitted primarily, but not exclusively on a single major haplotype that behaves functionally in a situation similar to that of compound heterozygozity.

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SUMMARYWe have studied ihe rote of macrophages in the produclion of IgG anli-DNA autoanlibodies by (NZBx NZW)F1 tnice(B/W). One of the main features of the syslemic lupus cryibematosus (SLE)-like disease that aftects these mice, h ihe presence of circuialing IgG autoantibodies and immune complexes, which lead lo renal failure and death by the age of 8 -9 months. IgG autoantibodies are produced without in vitro siimulallon by lolal spleen eells from these miee when they reach tbe age of 6 monlhs. We have demonstrated ihat lL-6 increases ihe production of IgG autoantibodies in cultures of splenic purified B cells from the old B/W miee. The aim of this study was to show the involvement of macrophages in the production of lL-6 and consequently in the produclion of IgG anti-DNA antibodies in ritro. We show thai elimination of the macrophages by different treatments led to reduction ofthe content of IL-6 in ihe supernalants as well as of IgG anti-DNA autoantibodies. Addition of fresh, splenic or peritoneal macrophages restored the produclion of autoantibodies in macrophage-depleted cultures from old B/W miee. There were no ditferences in the capacity of IL-6 produelion between macrophages from old or young B/W miee. but an imporiani difference was observed between peritoneal and splenic maerophages, where the former produced mueh higher levels ol' IL-6, and eonsequently were more poleni inducers of IgG autoantibodies. The present results reinforee Ihe role of macrophages and lL-6 in Ihe production of IgG anti-DNA autoanlibodies in B/W mice. The implieations of these results in the pathogenesis of the disease are discussed.