Functional SNPs


SNP Position Alelle aP (PGC2) bP (CLOZUK) Location Nearby Genes Disrupted TFs
rs301792chr1:8468278A/G1.58e-083.17e-08intronicREREPOLR2A
rs159961chr1:8484228C/T6.85e-097.83e-09intronicREREREST
rs11263852chr1:36554442G/C1.07e-049.21e-05upstream;downstreamADPRHL2/TEKT2CTCF/RAD21/SIN3A
rs2231318chr1:36602943C/T3.68e-052.44e-04intronicTRAPPC3POLR2A
rs74105186chr1:97850060T/C5.82e-061.99e-06intronicDPYDRAD21
rs2027349chr1:150039678G/A1.73e-088.21e-09UTR5VPS45CTCF/TAF1
rs78681982chr1:150130096G/A8.15e-096.17e-09intronicPLEKHO1POLR2A
rs72694957chr1:150135291C/T3.09e-091.33e-09intergenicPLEKHO1/ANP32EREST
rs16937chr1:205035455A/G8.69e-071.45e-06intronicCNTN2CTCF
rs12136320chr1:205110946T/C2.11e-054.96e-05downstreamDSTYKCTCF/POLR2A/RAD21/SMC3
rs340836chr1:214163069C/T4.69e-064.94e-06intronicPROX1CTCF
rs3904682chr1:243419429T/A2.34e-069.88e-07UTR5SDCCAG8POLR2A
rs78751650chr10:64066544C/T4.34e-071.53e-06intergenicRTKN2/LOC283045REST
rs10786700chr10:104387735C/T1.01e-082.00e-10intronicSUFUREST
rs12416331chr10:104928914T/A4.59e-167.09e-18intronicNT5C2GATA3
rs12146541chr11:57508678G/C2.83e-074.77e-09ncRNA_intronicTMX2-CTNND1SMC3
rs494791chr11:82996986A/C8.11e-051.30e-04exonicCCDC90BPOLR2A
rs11233566chr11:83048096G/T8.57e-062.64e-05intergenicCCDC90B/DLG2POLR2A
rs3781884chr11:113217364A/G1.15e-053.96e-06intronicTTC12CTCF
rs10860964chr12:103596455T/C9.92e-083.49e-07intergenicLOC101929058/C12orf42RAD21
rs7304243chr12:110662327C/T7.66e-071.24e-09intergenicIFT81/ATP2A2POLR2A
rs78866909chr12:123722833C/T2.12e-061.05e-05intronicC12orf65CTCF/RAD21/SMC3
rs4759413chr12:123743436T/A2.06e-067.66e-06downstreamC12orf65POLR2A
rs76514049chr12:123752637G/A1.66e-067.93e-06intronicCDK2AP1YY1
rs60754073chr12:123849272C/G5.24e-062.13e-05downstreamMIR8072REST
rs28594416chr12:123849921T/C2.00e-065.94e-06upstreamMIR8072POLR2A
rs11160502chr14:99667179G/A8.13e-074.63e-07intronicBCL11BSMC3
rs10083370chr14:104314182G/A2.09e-103.44e-14ncRNA_intronicLINC00637POLR2A/TAF1
rs10083367chr14:104314183C/G3.63e-101.51e-12ncRNA_intronicLINC00637POLR2A/TAF1
rs62021888chr15:40583560G/T3.88e-064.82e-07exonicPLCB2CTCF
rs3743078chr15:78894759C/G2.03e-123.11e-12intronicCHRNA3POLR2A
rs71196093/rs72748702chr15:84915246A/G6.08e-091.15e-07intergenicGOLGA6L4/LOC103171574CTCF
rs12912934chr15:85114447C/T3.44e-102.27e-08ncRNA_exonicLINC00933CTCF/RAD21
rs10795chr15:85177297G/A3.76e-097.86e-08ncRNA_exonicSCAND2PCTCF
rs2856268chr15:89878391T/C8.99e-032.13e-02upstreamPOLGEP300
rs4932217chr15:89902032A/C2.56e-044.40e-03intergenicPOLG/MIR9-3HGMAX
rs4786494chr16:4506232G/A5.62e-054.62e-06UTR3DNAJA3POLR2A
rs2270363chr16:4526292A/G3.31e-053.57e-06intronicHMOX2MAX/USF1
rs3814880chr16:30017895T/C6.41e-103.93e-12intronicDOC2APOLR2A
rs11861362chr16:68418792C/G1.82e-062.76e-06intronicSMPD3RAD21
rs3096324chr16:89422823G/A6.27e-05intronicANKRD11CTCF
rs4785581chr16:89699664C/A3.10e-05intronicDPEP1MAX/USF1
rs4790347chr17:1288955G/A4.95e-063.94e-06intronicYWHAEPOLR2A
rs10852932chr17:2143460G/T6.99e-091.64e-09intronicSMG6EP300
rs4924832chr17:17897739T/C4.89e-083.04e-07intronicDRC3CTCF/SMC3
rs2974999chr17:17997547T/G3.65e-071.73e-06intronicDRG2CTCF/RAD21/USF1
rs78532287chr17:19912679A/G4.86e-034.05e-02UTR5SPECC1SMC3
rs61660810chr17:20170608C/T2.55e-017.65e-01intronicSPECC1EP300/NFIC
rs11081564chr18:77551586A/G3.39e-034.30e-04intergenicCTDP1/KCNG2REST/SIN3A
rs3794993chr19:19611550C/A5.41e-084.64e-11intronicGATAD2APOLR2A
rs2304206chr19:50168871G/A3.19e-061.07e-10UTR5BCL2L12ELF1
rs2304204chr19:50169020T/C1.74e-064.43e-11UTR5BCL2L12/IRF3POLR2A
rs13003881chr2:25352091G/A5.09e-051.05e-04intronicEFR3BPOLR2A
rs12473400chr2:28024024G/T1.00e-067.16e-07intronicRBKSPOLR2A
rs34419497chr2:73140851C/T3.16e-054.54e-06intergenicSPR/EMX1CTCF
rs74863866chr2:73339043G/A8.59e-055.52e-04intronicRAB11FIP5CTCF
rs41285977chr2:73461553C/T8.15e-061.09e-04intronicCCT7REST
rs7579996chr2:110371692C/A5.52e-052.66e-05UTR5SEPT10POLR2A/REST/SIN3A
rs796364chr2:200716119C/A5.89e-149.41e-17upstreamFTCDNL1CTCF/RAD21
rs281759chr2:200787719T/C4.72e-139.25e-16intronicC2orf69FOXP2
rs3769481chr2:201173620A/G1.22e-062.98e-06intronicSPATS2LCTCF/RAD21
rs2551945chr2:208481637C/T3.07e-055.58e-05intronicMETTL21AREST
rs2385395chr2:220049128G/T2.30e-061.70e-05UTR3FAM134APOLR2A
rs2675960chr2:233792109G/T1.61e-101.98e-12intronicNGEFEZH2
rs9611198chr22:39955873A/C2.76e-091.32e-11intergenicRPS19BP1/CACNA1ICTCF
rs732381chr22:40051166A/T2.15e-101.11e-11intronicCACNA1IGATA2
rs5751195chr22:42380001A/C2.54e-077.20e-10intronicSEPT3POLR2A
rs8135801chr22:42475568A/G4.31e-072.33e-09upstream;downstreamSMDT1/FAM109BPOLR2A
rs2269524chr22:42475703T/G4.50e-071.95e-09UTR5SMDT1POLR2A
rs1801311chr22:42486723G/A2.21e-071.47e-09exonicNDUFA6POLR2A/TAF1/YY1
rs6002621chr22:42511002A/C2.18e-071.14e-09ncRNA_intronicNDUFA6-AS1SMC3
rs28633410chr22:42527471T/C1.81e-079.63e-10upstreamCYP2D6/LOC101929829POLR2A
rs9306356chr22:42567090T/C6.92e-064.99e-07intronicTCF20POLR2A/REST
rs138833chr22:50178917A/G1.33e-052.63e-05intronicBRD1CTCF
rs910800chr22:50278642C/T1.02e-066.56e-07exonicZBED4RAD21
rs1321chr22:50297435T/C1.68e-061.25e-06UTR3ALG12GATA2
rs9616378chr22:50311973A/G7.32e-062.19e-06UTR5ALG12POLR2A/REST/SIN3A/TAF1
rs9616382chr22:50312979C/T2.53e-051.66e-05intronicCRELD2REST
rs7410601chr22:50317187C/T9.91e-065.27e-06intronicCRELD2CTCF
rs9985472chr3:17681459A/G5.97e-063.93e-06intronicTBC1D5USF1
rs13323091chr3:30076004C/G2.29e-061.30e-04intergenicRBMS3/TGFBR2POLR2A
rs28365992chr3:50340996T/C9.90e-019.16e-01UTR5HYAL1POLR2A
rs2535629chr3:52833219G/A1.33e-081.48e-07intronicITIH3CTCF
rs3773744chr3:53270344T/C1.23e-041.18e-07intronicTKTREST/SIN3A
rs3773745chr3:53270424A/T8.76e-059.47e-08intronicTKTPOLR2A/RAD21
rs6795127chr3:53376669C/T2.11e-051.60e-07intronicDCP1AREST
rs1499894chr3:71571696C/T3.48e-072.12e-08intronicFOXP1POLR2A
rs485315chr3:161473229C/T1.95e-062.88e-07intergenicOTOL1/LINC01192POLR2A
rs308699chr3:161488369G/A2.44e-071.57e-08intergenicOTOL1/LINC01192CTCF
rs34455584chr3:180630191A/G3.05e-102.93e-11upstreamFXR1CTCF/RAD21
rs1805579chr3:180630565T/C1.56e-106.20e-12intronicFXR1REST
rs7662342chr4:26805393G/A1.32e-047.52e-06intergenicTBC1D19/STIM2RAD21
rs393223chr4:103605916G/A3.68e-032.50e-03intronicMANBAPBX3
rs223390chr4:103748797A/G1.01e-041.24e-05UTR5UBE2D3REST
rs223387chr4:103749516C/G1.07e-041.29e-05ncRNA_intronicLOC105377348RAD21
rs13113099chr4:103974122A/G2.43e-032.60e-03intronicSLC9B2USF1
rs3797040chr4:170540857C/T4.35e-083.48e-07upstreamCLCN3TAF1
rs10940235chr5:49636753G/T1.01e-032.70e-04intergenicNONE/EMBPBX3
rs2438345chr5:90162285T/C1.56e-051.70e-04intronicADGRV1CTCF/RAD21/SMC3
rs10038801chr5:101769984T/C4.32e-061.59e-06intronicSLCO6A1CTCF/RAD21
rs790475chr5:127149861C/T8.03e-055.96e-05intergenicCTXN3/LINC01184REST
rs982085chr5:137775581C/G1.99e-071.03e-08intronicREEP2CTCF
rs778593chr5:140027216T/C9.53e-063.24e-06UTR5NDUFA2USF1
rs3822346chr5:140187322C/T1.86e-062.17e-06exonicPCDHA4CTCF
rs57336534chr5:151940238T/A6.37e-067.92e-07intergenicNMUR2/LINC01470REST
rs58848914chr5:153498135C/T2.73e-061.28e-06intergenicMFAP3/GALNT10SMC3
rs6871683chr5:153688215T/C4.62e-077.70e-06intronicGALNT10GATA2
rs3131340/rs115800871chr6:28779878T/G-1.12e-43intergenicZBED9/LINC01623REST
rs13193668chr6:65199887G/T5.51e-033.43e-02intronicEYSNFIC
rs9362397chr6:87861585C/T1.48e-047.20e-03intergenicCGA/ZNF292CTCF
rs117178087chr6:96464060C/T5.89e-083.44e-06UTR5FUT9CTCF/RAD21
rs3813498chr6:108944165C/T1.42e-063.88e-06intronicFOXO3CTCF
rs6919476chr6:112065298G/C2.57e-012.39e-01intronicFYNPOLR2A
rs61202914chr6:112194051G/A1.68e-022.80e-03intronicFYNCTCF
rs9373388chr6:143646783C/T2.15e-031.08e-04intronicAIG1FOSL2/PBX3
rs3804536chr6:143658860A/G2.06e-051.61e-07intronicAIG1CTCF/RAD21
rs2711116chr7:24595020T/C1.42e-045.65e-05intergenicNPY/MPP6CTCF
rs12665974chr7:24781824C/T1.51e-052.98e-07intronicDFNA5TEAD4
rs321964chr7:78315591G/A5.28e-031.70e-03intronicMAGI2PBX3
rs322004chr7:78332416T/A2.75e-057.77e-06intronicMAGI2POLR2A
rs2905232chr7:113392567C/G2.85e-028.30e-03intergenicLINC00998/PPP1R3ACTCF
rs7796648chr7:113460326T/C3.96e-022.09e-02intergenicLINC00998/PPP1R3APOLR2A
rs6992091chr8:8168222G/A1.29e-062.65e-04intergenicFAM86B3P/SGK223TCF12
rs7014953chr8:8168413A/C1.20e-062.25e-04intergenicFAM86B3P/SGK223USF1
rs486781chr8:8639740A/G6.31e-053.70e-03intergenicCLDN23/MFHAS1POLR2A
rs12114661chr8:9573154G/A5.71e-068.21e-05intronicTNKSPOLR2A
rs11986122chr8:10009949C/G1.99e-062.55e-05intronicMSRAREST
rs11993089chr8:10009952G/T4.68e-064.74e-05intronicMSRAPOLR2A/REST
rs1565231chr8:18413457A/G1.20e-066.00e-08intronicPSD3CTCF
rs716881chr8:89516441T/G8.24e-083.67e-07intergenicMMP16/LOC101929709EP300
rs1352318chr8:89566903G/A9.67e-073.64e-06intergenicMMP16/LOC101929709CTCF/RAD21/SMC3
rs7012106chr8:144815612C/G1.60e-044.55e-05intronicFAM83HCTCF
SNP Position Alelle aP (PGC2) bP (CLOZUK) Location Nearby Genes Disrupted TFs

Where does this data come from?

aP (PGC2) -Pvalue of this SNP from the PGC2 GWAS of schizophrenia. [PMID: 25056061]
bP (CLOZUK) -Pvalue 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]