Functional SNPs
| SNP | aPosition | Alelle | bP (PGC2) | cP (CLOZUK) | Location | Nearby Genes | Disrupted TFs |
|---|---|---|---|---|---|---|---|
| rs301792 | chr1:8468278 | A/G | 1.58e-08 | 3.17e-08 | intronic | RERE | POLR2A |
| rs159961 | chr1:8484228 | C/T | 6.85e-09 | 7.83e-09 | intronic | RERE | REST |
| rs11263852 | chr1:36554442 | G/C | 1.07e-04 | 9.21e-05 | upstream;downstream | ADPRHL2/TEKT2 | CTCF/RAD21/SIN3A |
| rs2231318 | chr1:36602943 | C/T | 3.68e-05 | 2.44e-04 | intronic | TRAPPC3 | POLR2A |
| rs74105186 | chr1:97850060 | T/C | 5.82e-06 | 1.99e-06 | intronic | DPYD | RAD21 |
| rs2027349 | chr1:150039678 | G/A | 1.73e-08 | 8.21e-09 | UTR5 | VPS45 | CTCF/TAF1 |
| rs78681982 | chr1:150130096 | G/A | 8.15e-09 | 6.17e-09 | intronic | PLEKHO1 | POLR2A |
| rs72694957 | chr1:150135291 | C/T | 3.09e-09 | 1.33e-09 | intergenic | PLEKHO1/ANP32E | REST |
| rs16937 | chr1:205035455 | A/G | 8.69e-07 | 1.45e-06 | intronic | CNTN2 | CTCF |
| rs12136320 | chr1:205110946 | T/C | 2.11e-05 | 4.96e-05 | downstream | DSTYK | CTCF/POLR2A/RAD21/SMC3 |
| rs340836 | chr1:214163069 | C/T | 4.69e-06 | 4.94e-06 | intronic | PROX1 | CTCF |
| rs3904682 | chr1:243419429 | T/A | 2.34e-06 | 9.88e-07 | UTR5 | SDCCAG8 | POLR2A |
| rs78751650 | chr10:64066544 | C/T | 4.34e-07 | 1.53e-06 | intergenic | RTKN2/LOC283045 | REST |
| rs10786700 | chr10:104387735 | C/T | 1.01e-08 | 2.00e-10 | intronic | SUFU | REST |
| rs12416331 | chr10:104928914 | T/A | 4.59e-16 | 7.09e-18 | intronic | NT5C2 | GATA3 |
| rs12146541 | chr11:57508678 | G/C | 2.83e-07 | 4.77e-09 | ncRNA_intronic | TMX2-CTNND1 | SMC3 |
| rs494791 | chr11:82996986 | A/C | 8.11e-05 | 1.30e-04 | exonic | CCDC90B | POLR2A |
| rs11233566 | chr11:83048096 | G/T | 8.57e-06 | 2.64e-05 | intergenic | CCDC90B/DLG2 | POLR2A |
| rs3781884 | chr11:113217364 | A/G | 1.15e-05 | 3.96e-06 | intronic | TTC12 | CTCF |
| rs10860964 | chr12:103596455 | T/C | 9.92e-08 | 3.49e-07 | intergenic | LOC101929058/C12orf42 | RAD21 |
| rs7304243 | chr12:110662327 | C/T | 7.66e-07 | 1.24e-09 | intergenic | IFT81/ATP2A2 | POLR2A |
| rs78866909 | chr12:123722833 | C/T | 2.12e-06 | 1.05e-05 | intronic | C12orf65 | CTCF/RAD21/SMC3 |
| rs4759413 | chr12:123743436 | T/A | 2.06e-06 | 7.66e-06 | downstream | C12orf65 | POLR2A |
| rs76514049 | chr12:123752637 | G/A | 1.66e-06 | 7.93e-06 | intronic | CDK2AP1 | YY1 |
| rs60754073 | chr12:123849272 | C/G | 5.24e-06 | 2.13e-05 | downstream | MIR8072 | REST |
| rs28594416 | chr12:123849921 | T/C | 2.00e-06 | 5.94e-06 | upstream | MIR8072 | POLR2A |
| rs11160502 | chr14:99667179 | G/A | 8.13e-07 | 4.63e-07 | intronic | BCL11B | SMC3 |
| rs10083370 | chr14:104314182 | G/A | 2.09e-10 | 3.44e-14 | ncRNA_intronic | LINC00637 | POLR2A/TAF1 |
| rs10083367 | chr14:104314183 | C/G | 3.63e-10 | 1.51e-12 | ncRNA_intronic | LINC00637 | POLR2A/TAF1 |
| rs62021888 | chr15:40583560 | G/T | 3.88e-06 | 4.82e-07 | exonic | PLCB2 | CTCF |
| rs3743078 | chr15:78894759 | C/G | 2.03e-12 | 3.11e-12 | intronic | CHRNA3 | POLR2A |
| rs71196093/rs72748702 | chr15:84915246 | A/G | 6.08e-09 | 1.15e-07 | intergenic | GOLGA6L4/LOC103171574 | CTCF |
| rs12912934 | chr15:85114447 | C/T | 3.44e-10 | 2.27e-08 | ncRNA_exonic | LINC00933 | CTCF/RAD21 |
| rs10795 | chr15:85177297 | G/A | 3.76e-09 | 7.86e-08 | ncRNA_exonic | SCAND2P | CTCF |
| rs2856268 | chr15:89878391 | T/C | 8.99e-03 | 2.13e-02 | upstream | POLG | EP300 |
| rs4932217 | chr15:89902032 | A/C | 2.56e-04 | 4.40e-03 | intergenic | POLG/MIR9-3HG | MAX |
| rs4786494 | chr16:4506232 | G/A | 5.62e-05 | 4.62e-06 | UTR3 | DNAJA3 | POLR2A |
| rs2270363 | chr16:4526292 | A/G | 3.31e-05 | 3.57e-06 | intronic | HMOX2 | MAX/USF1 |
| rs3814880 | chr16:30017895 | T/C | 6.41e-10 | 3.93e-12 | intronic | DOC2A | POLR2A |
| rs11861362 | chr16:68418792 | C/G | 1.82e-06 | 2.76e-06 | intronic | SMPD3 | RAD21 |
| rs3096324 | chr16:89422823 | G/A | 6.27e-05 | intronic | ANKRD11 | CTCF | |
| rs4785581 | chr16:89699664 | C/A | 3.10e-05 | intronic | DPEP1 | MAX/USF1 | |
| rs4790347 | chr17:1288955 | G/A | 4.95e-06 | 3.94e-06 | intronic | YWHAE | POLR2A |
| rs10852932 | chr17:2143460 | G/T | 6.99e-09 | 1.64e-09 | intronic | SMG6 | EP300 |
| rs4924832 | chr17:17897739 | T/C | 4.89e-08 | 3.04e-07 | intronic | DRC3 | CTCF/SMC3 |
| rs2974999 | chr17:17997547 | T/G | 3.65e-07 | 1.73e-06 | intronic | DRG2 | CTCF/RAD21/USF1 |
| rs78532287 | chr17:19912679 | A/G | 4.86e-03 | 4.05e-02 | UTR5 | SPECC1 | SMC3 |
| rs61660810 | chr17:20170608 | C/T | 2.55e-01 | 7.65e-01 | intronic | SPECC1 | EP300/NFIC |
| rs11081564 | chr18:77551586 | A/G | 3.39e-03 | 4.30e-04 | intergenic | CTDP1/KCNG2 | REST/SIN3A |
| rs3794993 | chr19:19611550 | C/A | 5.41e-08 | 4.64e-11 | intronic | GATAD2A | POLR2A |
| rs2304206 | chr19:50168871 | G/A | 3.19e-06 | 1.07e-10 | UTR5 | BCL2L12 | ELF1 |
| rs2304204 | chr19:50169020 | T/C | 1.74e-06 | 4.43e-11 | UTR5 | BCL2L12/IRF3 | POLR2A |
| rs13003881 | chr2:25352091 | G/A | 5.09e-05 | 1.05e-04 | intronic | EFR3B | POLR2A |
| rs12473400 | chr2:28024024 | G/T | 1.00e-06 | 7.16e-07 | intronic | RBKS | POLR2A |
| rs34419497 | chr2:73140851 | C/T | 3.16e-05 | 4.54e-06 | intergenic | SPR/EMX1 | CTCF |
| rs74863866 | chr2:73339043 | G/A | 8.59e-05 | 5.52e-04 | intronic | RAB11FIP5 | CTCF |
| rs41285977 | chr2:73461553 | C/T | 8.15e-06 | 1.09e-04 | intronic | CCT7 | REST |
| rs7579996 | chr2:110371692 | C/A | 5.52e-05 | 2.66e-05 | UTR5 | SEPT10 | POLR2A/REST/SIN3A |
| rs796364 | chr2:200716119 | C/A | 5.89e-14 | 9.41e-17 | upstream | FTCDNL1 | CTCF/RAD21 |
| rs281759 | chr2:200787719 | T/C | 4.72e-13 | 9.25e-16 | intronic | C2orf69 | FOXP2 |
| rs3769481 | chr2:201173620 | A/G | 1.22e-06 | 2.98e-06 | intronic | SPATS2L | CTCF/RAD21 |
| rs2551945 | chr2:208481637 | C/T | 3.07e-05 | 5.58e-05 | intronic | METTL21A | REST |
| rs2385395 | chr2:220049128 | G/T | 2.30e-06 | 1.70e-05 | UTR3 | FAM134A | POLR2A |
| rs2675960 | chr2:233792109 | G/T | 1.61e-10 | 1.98e-12 | intronic | NGEF | EZH2 |
| rs9611198 | chr22:39955873 | A/C | 2.76e-09 | 1.32e-11 | intergenic | RPS19BP1/CACNA1I | CTCF |
| rs732381 | chr22:40051166 | A/T | 2.15e-10 | 1.11e-11 | intronic | CACNA1I | GATA2 |
| rs5751195 | chr22:42380001 | A/C | 2.54e-07 | 7.20e-10 | intronic | SEPT3 | POLR2A |
| rs8135801 | chr22:42475568 | A/G | 4.31e-07 | 2.33e-09 | upstream;downstream | SMDT1/FAM109B | POLR2A |
| rs2269524 | chr22:42475703 | T/G | 4.50e-07 | 1.95e-09 | UTR5 | SMDT1 | POLR2A |
| rs1801311 | chr22:42486723 | G/A | 2.21e-07 | 1.47e-09 | exonic | NDUFA6 | POLR2A/TAF1/YY1 |
| rs6002621 | chr22:42511002 | A/C | 2.18e-07 | 1.14e-09 | ncRNA_intronic | NDUFA6-AS1 | SMC3 |
| rs28633410 | chr22:42527471 | T/C | 1.81e-07 | 9.63e-10 | upstream | CYP2D6/LOC101929829 | POLR2A |
| rs9306356 | chr22:42567090 | T/C | 6.92e-06 | 4.99e-07 | intronic | TCF20 | POLR2A/REST |
| rs138833 | chr22:50178917 | A/G | 1.33e-05 | 2.63e-05 | intronic | BRD1 | CTCF |
| rs910800 | chr22:50278642 | C/T | 1.02e-06 | 6.56e-07 | exonic | ZBED4 | RAD21 |
| rs1321 | chr22:50297435 | T/C | 1.68e-06 | 1.25e-06 | UTR3 | ALG12 | GATA2 |
| rs9616378 | chr22:50311973 | A/G | 7.32e-06 | 2.19e-06 | UTR5 | ALG12 | POLR2A/REST/SIN3A/TAF1 |
| rs9616382 | chr22:50312979 | C/T | 2.53e-05 | 1.66e-05 | intronic | CRELD2 | REST |
| rs7410601 | chr22:50317187 | C/T | 9.91e-06 | 5.27e-06 | intronic | CRELD2 | CTCF |
| rs9985472 | chr3:17681459 | A/G | 5.97e-06 | 3.93e-06 | intronic | TBC1D5 | USF1 |
| rs13323091 | chr3:30076004 | C/G | 2.29e-06 | 1.30e-04 | intergenic | RBMS3/TGFBR2 | POLR2A |
| rs28365992 | chr3:50340996 | T/C | 9.90e-01 | 9.16e-01 | UTR5 | HYAL1 | POLR2A |
| rs2535629 | chr3:52833219 | G/A | 1.33e-08 | 1.48e-07 | intronic | ITIH3 | CTCF |
| rs3773744 | chr3:53270344 | T/C | 1.23e-04 | 1.18e-07 | intronic | TKT | REST/SIN3A |
| rs3773745 | chr3:53270424 | A/T | 8.76e-05 | 9.47e-08 | intronic | TKT | POLR2A/RAD21 |
| rs6795127 | chr3:53376669 | C/T | 2.11e-05 | 1.60e-07 | intronic | DCP1A | REST |
| rs1499894 | chr3:71571696 | C/T | 3.48e-07 | 2.12e-08 | intronic | FOXP1 | POLR2A |
| rs485315 | chr3:161473229 | C/T | 1.95e-06 | 2.88e-07 | intergenic | OTOL1/LINC01192 | POLR2A |
| rs308699 | chr3:161488369 | G/A | 2.44e-07 | 1.57e-08 | intergenic | OTOL1/LINC01192 | CTCF |
| rs34455584 | chr3:180630191 | A/G | 3.05e-10 | 2.93e-11 | upstream | FXR1 | CTCF/RAD21 |
| rs1805579 | chr3:180630565 | T/C | 1.56e-10 | 6.20e-12 | intronic | FXR1 | REST |
| rs7662342 | chr4:26805393 | G/A | 1.32e-04 | 7.52e-06 | intergenic | TBC1D19/STIM2 | RAD21 |
| rs393223 | chr4:103605916 | G/A | 3.68e-03 | 2.50e-03 | intronic | MANBA | PBX3 |
| rs223390 | chr4:103748797 | A/G | 1.01e-04 | 1.24e-05 | UTR5 | UBE2D3 | REST |
| rs223387 | chr4:103749516 | C/G | 1.07e-04 | 1.29e-05 | ncRNA_intronic | LOC105377348 | RAD21 |
| rs13113099 | chr4:103974122 | A/G | 2.43e-03 | 2.60e-03 | intronic | SLC9B2 | USF1 |
| rs3797040 | chr4:170540857 | C/T | 4.35e-08 | 3.48e-07 | upstream | CLCN3 | TAF1 |
| rs10940235 | chr5:49636753 | G/T | 1.01e-03 | 2.70e-04 | intergenic | NONE/EMB | PBX3 |
| rs2438345 | chr5:90162285 | T/C | 1.56e-05 | 1.70e-04 | intronic | ADGRV1 | CTCF/RAD21/SMC3 |
| rs10038801 | chr5:101769984 | T/C | 4.32e-06 | 1.59e-06 | intronic | SLCO6A1 | CTCF/RAD21 |
| rs790475 | chr5:127149861 | C/T | 8.03e-05 | 5.96e-05 | intergenic | CTXN3/LINC01184 | REST |
| rs982085 | chr5:137775581 | C/G | 1.99e-07 | 1.03e-08 | intronic | REEP2 | CTCF |
| rs778593 | chr5:140027216 | T/C | 9.53e-06 | 3.24e-06 | UTR5 | NDUFA2 | USF1 |
| rs3822346 | chr5:140187322 | C/T | 1.86e-06 | 2.17e-06 | exonic | PCDHA4 | CTCF |
| rs57336534 | chr5:151940238 | T/A | 6.37e-06 | 7.92e-07 | intergenic | NMUR2/LINC01470 | REST |
| rs58848914 | chr5:153498135 | C/T | 2.73e-06 | 1.28e-06 | intergenic | MFAP3/GALNT10 | SMC3 |
| rs6871683 | chr5:153688215 | T/C | 4.62e-07 | 7.70e-06 | intronic | GALNT10 | GATA2 |
| rs3131340/rs115800871 | chr6:28779878 | T/G | - | 1.12e-43 | intergenic | ZBED9/LINC01623 | REST |
| rs13193668 | chr6:65199887 | G/T | 5.51e-03 | 3.43e-02 | intronic | EYS | NFIC |
| rs9362397 | chr6:87861585 | C/T | 1.48e-04 | 7.20e-03 | intergenic | CGA/ZNF292 | CTCF |
| rs117178087 | chr6:96464060 | C/T | 5.89e-08 | 3.44e-06 | UTR5 | FUT9 | CTCF/RAD21 |
| rs3813498 | chr6:108944165 | C/T | 1.42e-06 | 3.88e-06 | intronic | FOXO3 | CTCF |
| rs6919476 | chr6:112065298 | G/C | 2.57e-01 | 2.39e-01 | intronic | FYN | POLR2A |
| rs61202914 | chr6:112194051 | G/A | 1.68e-02 | 2.80e-03 | intronic | FYN | CTCF |
| rs9373388 | chr6:143646783 | C/T | 2.15e-03 | 1.08e-04 | intronic | AIG1 | FOSL2/PBX3 |
| rs3804536 | chr6:143658860 | A/G | 2.06e-05 | 1.61e-07 | intronic | AIG1 | CTCF/RAD21 |
| rs2711116 | chr7:24595020 | T/C | 1.42e-04 | 5.65e-05 | intergenic | NPY/MPP6 | CTCF |
| rs12665974 | chr7:24781824 | C/T | 1.51e-05 | 2.98e-07 | intronic | DFNA5 | TEAD4 |
| rs321964 | chr7:78315591 | G/A | 5.28e-03 | 1.70e-03 | intronic | MAGI2 | PBX3 |
| rs322004 | chr7:78332416 | T/A | 2.75e-05 | 7.77e-06 | intronic | MAGI2 | POLR2A |
| rs2905232 | chr7:113392567 | C/G | 2.85e-02 | 8.30e-03 | intergenic | LINC00998/PPP1R3A | CTCF |
| rs7796648 | chr7:113460326 | T/C | 3.96e-02 | 2.09e-02 | intergenic | LINC00998/PPP1R3A | POLR2A |
| rs6992091 | chr8:8168222 | G/A | 1.29e-06 | 2.65e-04 | intergenic | FAM86B3P/SGK223 | TCF12 |
| rs7014953 | chr8:8168413 | A/C | 1.20e-06 | 2.25e-04 | intergenic | FAM86B3P/SGK223 | USF1 |
| rs486781 | chr8:8639740 | A/G | 6.31e-05 | 3.70e-03 | intergenic | CLDN23/MFHAS1 | POLR2A |
| rs12114661 | chr8:9573154 | G/A | 5.71e-06 | 8.21e-05 | intronic | TNKS | POLR2A |
| rs11986122 | chr8:10009949 | C/G | 1.99e-06 | 2.55e-05 | intronic | MSRA | REST |
| rs11993089 | chr8:10009952 | G/T | 4.68e-06 | 4.74e-05 | intronic | MSRA | POLR2A/REST |
| rs1565231 | chr8:18413457 | A/G | 1.20e-06 | 6.00e-08 | intronic | PSD3 | CTCF |
| rs716881 | chr8:89516441 | T/G | 8.24e-08 | 3.67e-07 | intergenic | MMP16/LOC101929709 | EP300 |
| rs1352318 | chr8:89566903 | G/A | 9.67e-07 | 3.64e-06 | intergenic | MMP16/LOC101929709 | CTCF/RAD21/SMC3 |
| rs7012106 | chr8:144815612 | C/G | 1.60e-04 | 4.55e-05 | intronic | FAM83H | CTCF |
| SNP | Position | Alelle | aP (PGC2) | bP (CLOZUK) | Location | Nearby Genes | Disrupted TFs |
Where does this data come from?
| aPosition | -Position was based on hg19 genome assembly. |
| bP (PGC2) | -P-value of this SNP from the PGC2 GWAS of schizophrenia. [PMID: 25056061] |
| cP (CLOZUK) | -P-value of this SNP from the CLOZUK GWAS of schizophrenia. [PMID: 29483656] |
We systematically investigate the gene regulatory mechanisms underpinning schizophrenia risk through integrating data from functional genomics (including 30 ChIP-Seq experiments) and position weight matrix (PWM). We identify 132 risk SNPs that disrupt transcription factor binding and we find that 97 of the 132 TF binding-disrupting SNPs are associated with gene expression in human brain tissues. [PMID: 30737407]