TABLE IV. List of Putative Transcription-Factor Binding Sites Modified by SNAP25 Schizophrenia-Associated SNPs in the Family Sample.
| SNP | Position (bp)a | Allele change | Gain/loss | Vertebrate matrix | Position (bp) | Strand | Name | Matrix simb | REc |
|---|---|---|---|---|---|---|---|---|---|
| SNP 3 (rs6077693) | 10154917 | A→G | Loss | V$FAST/FAST1.02 | 10154910–10154926 | − | Forkhead box H1 (Foxh1) | 0.950 | 0.03 |
| SNP 11 (rs362562) | 10191186 | A→G | Loss | VSGFI1/GFI1.02 | 10191177–10191191 | − | Growth factor independence 1 | 0.963 | 1.29 |
| Loss | V$HOXC/PBX_HOXA9.01 | 10191180–10191196 | + | PBX-HOXA9 binding site | 0.804 | 0.01 | |||
| Gain | V$CAAT/CAAT.01 | 10191176–10191190 | − | Cellular and viral CCAAT box | 0.900 | 2.35 | |||
| Gain | V$HAML/AML3.01 | 10191179–10191193 | + | Runt-related transcription factor 2/CBFA1 (core-binding factor, runt domain, alpha subunit 1) | 0.945 | 0.11 | |||
| SNP 15 (rs362988) | 10229370 | A→G | Loss | V$CLOX/CDPCR3HD.01 | 10229355–10229377 | − | Cut-like homeodomain protein (cut repeat III/homeodomain) | 0.961 | 3.06 |
| Loss | V$CLOX/CLOX.01 | 10229360–10229382 | + | Cut-like homeodomain protein | 0.888 | 0.14 | |||
| SNP 16 (rs362988) | 10230027 | C→T | Loss | V$XBBF/MIF1.01 | 10230027–10230055 | − | MIBP1/RFX1 complex | 0.762 | 0.01 |
| Gain | V$HOMF/S8.01 | 10230015–10230031 | + | Binding site for S8 type homeodomains | 0.997 | 1.90 | |||
| Gain | V$LHXF/LMX1B.01 | 10230016–10230032 | + | LIM-homeodomain transcription factor | 0.918 | 0.09 | |||
| Gain | V$BRNF/BRN3.02 | 10230017–10230035 | + | Brn-3, POU-IV protein class | 0.921 | 1.62 | |||
| Gain | V$HOXF/GSH2.01 | 10230017–10230033 | − | Homeodomain transcription factor Gsh-2 | 0.952 | 1.84 | |||
| Gain | V$OCTP/OCT1P.01 | 10230017–10230029 | − | Octamer-binding factor-1, POU specific domain | 0.875 | 0.61 | |||
| Gain | V$BRNF/BRN3.01 | 10230018–10230036 | − | Brn-3, POU-IV protein class | 0.792 | 0.00 | |||
| Gain | V$HOXF/GSH1.01 | 10230020–10230036 | − | Homeobox transcription factor Gsh-1 | 0.899 | 0.14 | |||
| Gain | V$HOXF/GSH2.01 | 10230020–10230036 | + | Homeodomain transcription factor Gsh-2 | 0.955 | 1.84 | |||
| Gain | V$LHXF/LMX1B.01 | 10230021–10230037 | − | LIM-homeodomain transcription factor | 0.932 | 0.09 | |||
| Gain | V$ATBF/ATBF1.01 | 10230022–10230038 | − | AT-binding transcription factor 1 | 0.830 | 0.07 | |||
| Gain | V$HOMF/8.01 | 10230022–10230038 | − | Binding site for S8 type homeodomain | 0.992 | 1.90 |
a
Human genome build 36.1.
b
Matrix similarity: A perfect match to the matrix gets a score of 1.00—a “good” match to the matrix usually has a similarity ≥ 0.80.
c
Random expectation (matches per 1,000 bp).