Intron 13 of the LTF Gene Contains Three SNPs Associated with ASM in cis (adapted from Schalkwyk et al, 2010). (A) Location of SNP_A-1972595 (rs6441990), SNP_A-2149420 (rs6441991), and SNP_A-1876897 (rs6441992) with the average RAS change across heterozygous individuals shown as blue bars. (B) Heat map of normalized array signal data for the three probes representing SNP_A-1972595 (rs6441990), demonstrating a consistent loss of heterozygosity following MSRE digestion. (C and D) Microarray data were verified using SNuPE analyses. Shown are examples for (C) (SNP_A-1972595 [rs6441990]) and (D) (SNP_A-2149420 [rs6441991]). (E and F) cis-acting ASM was confirmed in the 30 CEPH family trios. Shown are data for (E) (SNP_A-1972595 [rs6441990]) and (F) (SNP_A-2149420 [rs6441991]). (G) Clonal bisulfite sequencing confirmed that G-A-A haplotypes are associated with lower DNA methylation (10%) compared to C-T-T haplotypes for four CpG sites spanning the three SNPs, including an informative HpaII site.