Fig. S3.

Predicted transcription factors overlapping SNPs rs116160149 and rs115388857. (A) ChIP-seq peaks of the transcription factors USF1 and RUNX3 on the promoter of LOC100294145 in the GM12878 lymphoblastoid cell line, at a genomic region overlapping AD-associated SNPs rs116160149. The ChIP-seq data is retrieved from RegulomeDB. (B) Sequence logo diagram retrieved from JASPER (https://jaspar.genereg.net/) showing frequency matrix profiles of BHLHE40 and USF1 transcription factor binding motifs. The letters represent the possible bases at respective positions in the motif, where the height of the letter indicates the frequency of the nucleotide observed in that position. Variants with higher nucleotide frequency increases the motif score and hence the likelihood of the transcription factor binding to the site. Black arrow indicates position of respective SNP of interest