1 319 633 0

3882 + 633 = 93.7%

−1 4848 correspondence −2 Log fold changes set 2

3882 11 −3

−3 −2 −1 0 1 Log fold changes set 1

Suppl. Fig. 1. Replication of sex differential methylation. A scatter-plot shows the concordance between the effect size from set 1 (x-axis, 485 patients, 30.5% female) and set 2 (y-axis, 190 patients 16.8% female). The number in each quadrant indicates the dots in each quadrant. wnstream (2−3kb) wnstream (<1kb) wnstream (1−2kb) 12 Distal Intergenic Promoter (<=1kb) Intron Promoter (1−2kb) Exon Promoter (2−3kb) 3' UTR D o D o D o MIR153−2 10 Distal Intergenic Promoter (<=1kb) Intron Promoter (1−2kb) 3' UTR Exon GALNT9 SLC17A7 SLC17A7 RTP5 8 GALNT9 LINC01012 CRIPAK 6 APBA2 DIP2C GJA3 ALX4 SRCIN1 4 ASIC4 ATP5MC2 TFAP2A HOXC6 2 SIX3 ITPKA PAX2 CACNA1A 0 NR2E1 SOX1 LINC02593 FOXF2 UNCX FAM20C ZIC5 HOXC6 C1QTNF8 ZIC4 CELF4 PEX10 HLX NRXN2 FBRSL1 CELF4 FBRSL1 APBA2 ALX4 MIR153−2 SIM2 HOXA4 LOC100129917 PAX6 DIP2C LOC283731 DMRT2 RTP5 MEG3 ADM LINC01005 COL9A1 NRXN2 PDE6B LRMDA KALRN LINC01012 GFI1 CRIPAK CDX1 OXT PRDM9 SPON2 ATP5MC2 HOXB3 TMEM190 TRPC3 SP6 GDF2 BNC1 Suppl. Fig. 2. Top genes sexDMPs. NKX6−3 SOGA3 A heatmap shows the number of genes FBXO47 ALDH1A3 mapped to by sexDMPs more methyl- NKX2−5 ated in males (top) and in females (right) LINC01101 LHX8 with genes on the rows and the location VAX2 LBX1−AS1 on the columns. Only genes that are at UNCX least mapped to by at least 5 sexDMPs TMEM174 20 HOTTIP are shown. TMEM33 PROX1 DMBX1 15 DDX18 MIR4776−1 PAX2 LOC648987 10 NCR2 ACTRT2 TBCA 5 SOX1 SIX3 0 no staining minor staining yes (A) moderate staining (B) (C) no heavy staining Macrophages Intraplaque hemorrhage

Smooth muscle cells 1.0 1.0 1.0 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0.0 0.0 0.0 female male female male female male minor staining no fat (D) (E) moderate staining (F) < 40% fat Collagen heavy staining Fat > 40% fat Vessel density 1.0 1.0 0.8 0.8 40 0.6 0.6 30 0.4 0.4 20 0.2 10 0.2 0 0.0 0.0 female male female male female male

Suppl. Fig. 3. Sex differences in plaque characteristics. A-F show smooth muscle cell content, macrophage staining, presence of intraplaque hemorrhage, vessel density, collagen staining and fat percentage, respectively, in female (left of each panel) and male (right of each panel) samples. 1 Beta value

0.8 Suppl. Fig. 4. Sex DMPs and celltypes. A) A heatmap shows the DNA methylation 0.6 pattern of the sexDMPs over the decon- voluted cell-types. The rows contain the 0.4 sexDMPs, the columns show the cell-type. B) The same heatmap as A) is shown, 0.2 but this one is clustered by k-means clus- tering (k = 7). C) A dotplot is shown for 0 enrichments for the k- means sexDMP clusters. Terms are allocated to the rows, color indicates significance, and size of the dot indicates the ratio of genes from the set present. The number indicates the number of genes that could be found in any of the 6 7 5 4 2 1 3 sets tested. Celltypes

Beta value Cluster: 3 0.8 Size: 682 Cluster: 5 Size: 644 0.6 Cluster: 7 Size: 583 0.4 Cluster: 2 Size: 1028 0.2 Cluster: 4 Size: 915 Cluster: 1 Size: 382 Cluster: 6 Size: 614 6 7 1 4 5 2 3 Celltypes

cell fate commitment GeneRatio 0.04 embryonic organ morphogenesis 0.06 pattern specification process 0.08 regionalization 0.10 embryonic organ development sensory organ morphogenesis p.adjust

gland development 0.01 embryonic skeletal system development 0.02 muscle organ development 0.03 0.04 central nervous system neuron differentiation 2 3 4 5 6 7 (651)(489)(608)(421)(404)(396) Clusters Promoter sexDMPs Distal sexDMPs 0.030 0.008 0.020 = 0.09 < 1e-4 perm perm 0.004 p p 0.010 Density Density 0.000 0.000 0 100 200 300 400 0 20 40 60 80 120 Number of regulatory links Number of regulatory links based on sexDMPs based on sexDMPs

Suppl. Fig. 5. Regulatory loci and location of sexDMPs. A density plot shows the permuted distribution of regulatory links based on promoter sexDMPs (left) and distal intergenic sexDMPs (right) with random genes. The vertical red line indicates the number of regulatory links to autosomal female-biased genes.