Figure 1.

Gene expression and variation at chr21q22. (A) Screen shots of selected tracks from the FANTOM5 Human hg38 promoterome (https://fantom.gsc.riken.jp/zenbu/) for the ETS2-PSMG1 interval. The upper track highlights the three spliced LINC RNAs transcribed in this interval. The promoter tags show peaks of capped 5’ end mRNA tags (CAGE) with green indicating forward and purple reverse orientation. Selecting the interval on the FANTOM5 Zenbu browser (https://fantom.gsc.riken.jp/zenbu/) reveals an expression table showing highest expression in monocytes (not shown). The zoomed interval highlights the close association between rs2836882 (Chr21:39094644) and enhancer-associated CAGE tags. (B) Haplotype variation associated with ethnicity in the ETS2-PSMG1 interval. Relationships between rs2836882 and rs2836754 in Europeans, Africans and South and East Asians were analysed using LDpair on https://ldlink.nih.gov. (C) The relationship between rs2836882 SNV genotype and ETS2 expression in MDM derived from member of IBD families (black; unaffected individual, n = 25; red affected individual, n = 25; blue healthy controls with no family history of IBD, n = 6). No differences are significant. Expression was similarly unrelated to rs2836754 genotype (not shown). (D) Alignment of mouse and human genomic DNA sequences in the vicinity of rs2836882. The red asterisk highlights the SNV (G in the major allele, A in the minor allele). Purple highlights the extended AP1-like element that is identical to the X2 box of HLA-DRA. Green highlights predicted STAT1,2 binding sites. Blue highlights conserved motif including a PU.1 consensus site (GAGGAA).