Analysis of transcription factor binding recognition sites

To predict the effect of the regulatory mutation rs41310367, we queried the sequence flanking the SNP with and without the variant for transcription factor binding site recognition motifs using the JASPAR database[26]. For the input sequences, we used the reference sequence AAGACCACGTCAC, the alternative reference sequence based on conservation AAGACCAGGTCAC, and the variant sequence AAGACCATGTCAC. Only recognition scores greater than 86 were considered for the initial analysis and then a threshold of 70 was set to determine the score after a sequence change that caused the score to be below 86.