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{"sheet":"Sheet1","index":0,"n_rows":236,"n_cols":11,"rows_kept":236,"cut":false,"hidden":false,"merged":[[0,1,0,4],[228,8,229,8],[230,8,231,8],[97,10,100,10],[77,8,78,8],[235,1,235,6],[63,3,64,3],[63,8,64,8],[61,8,62,8],[63,10,64,10],[101,3,104,3],[101,8,104,8],[101,10,104,10],[75,3,76,3],[75,8,76,8],[75,10,76,10],[77,3,78,3],[77,10,78,10],[81,3,84,3],[81,8,84,8],[81,10,84,10],[97,3,100,3],[97,8,100,8],[85,3,88,3],[224,8,225,8],[226,8,227,8],[85,10,88,10],[89,3,92,3],[89,8,92,8],[89,10,92,10],[93,3,96,3],[55,3,56,3],[55,8,56,8],[57,3,58,3],[57,8,58,8],[57,10,58,10],[59,3,60,3],[59,8,60,8],[59,10,60,10],[61,3,62,3],[61,10,62,10],[93,8,96,8],[93,10,96,10],[105,3,108,3],[105,8,108,8],[105,10,108,10],[123,3,124,3],[25,8,26,8],[25,10,26,10],[23,2,24,2],[23,3,24,3],[49,3,50,3],[49,8,50,8],[47,8,48,8],[45,8,46,8],[43,8,44,8],[41,8,42,8],[39,8,40,8],[37,8,38,8],[49,10,50,10],[39,10,40,10],[41,3,42,3],[41,10,42,10],[43,3,44,3],[43,10,44,10],[45,3,46,3],[45,10,46,10],[47,3,48,3],[47,10,48,10],[39,3,40,3],[230,1,231,1],[230,2,231,2],[222,1,223,1],[222,2,223,2],[224,1,225,1],[224,2,225,2],[17,8,18,8],[21,8,22,8],[17,10,18,10],[21,10,22,10],[19,1,20,1],[19,2,20,2],[19,3,20,3],[19,8,20,8],[19,10,20,10],[17,2,18,2],[17,3,18,3],[21,2,22,2],[21,3,22,3],[23,8,24,8],[23,10,24,10],[25,1,26,1],[25,2,26,2],[123,8,124,8],[25,3,26,3],[65,1,66,1],[71,0,72,0],[226,1,227,1],[226,2,227,2],[228,1,229,1],[228,2,229,2],[183,1,184,1],[183,2,184,2],[208,1,209,1],[208,2,209,2],[218,1,219,1],[218,2,219,2],[175,2,176,2],[181,1,182,1],[181,2,182,2],[177,2,178,2],[117,2,120,2],[75,2,76,2],[101,2,104,2],[89,1,92,1],[89,2,92,2],[81,2,84,2],[85,1,88,1],[11,0,16,0],[45,1,46,1],[30,0,32,0],[39,1,40,1],[33,0,34,0],[35,0,56,0],[35,1,36,1],[17,0,18,0],[17,1,18,1],[23,1,24,1],[43,1,44,1],[19,0,22,0],[21,1,22,1],[23,0,26,0],[41,1,42,1],[47,1,48,1],[37,1,38,1],[2,0,5,0],[199,0,207,0],[190,0,198,0],[131,0,135,0],[136,0,137,0],[136,1,137,1],[136,2,137,2],[138,0,174,0],[51,1,52,1],[51,2,52,2],[175,1,176,1],[77,1,78,1],[175,0,188,0],[187,1,188,1],[187,2,188,2],[185,1,186,1],[185,2,186,2],[75,0,78,0],[61,2,62,2],[77,2,78,2],[75,1,76,1],[61,1,62,1],[6,0,9,0],[27,0,29,0],[179,1,180,1],[179,2,180,2],[85,2,88,2],[113,1,116,1],[113,2,116,2],[97,1,100,1],[97,2,100,2],[101,1,104,1],[123,1,124,1],[123,2,124,2],[105,1,108,1],[105,2,108,2],[67,0,70,0],[57,1,58,1],[37,2,38,2],[43,2,44,2],[53,2,54,2],[177,1,178,1],[47,2,48,2],[45,2,46,2],[57,0,66,0],[57,2,58,2],[59,1,60,1],[59,2,60,2],[63,1,64,1],[63,2,64,2],[49,1,50,1],[49,2,50,2],[53,1,54,1],[39,2,40,2],[55,1,56,1],[55,2,56,2],[109,1,112,1],[109,2,112,2],[81,0,120,0],[81,1,84,1],[109,3,112,3],[109,8,112,8],[109,10,112,10],[35,3,36,3],[35,8,36,8],[37,3,38,3],[37,10,38,10],[93,1,96,1],[93,2,96,2],[65,3,66,3],[65,8,66,8],[65,10,66,10],[51,3,52,3],[51,10,52,10],[53,3,54,3],[51,8,52,8],[53,8,54,8],[53,10,54,10],[55,10,56,10],[35,2,36,2],[41,2,42,2],[65,2,66,2],[35,10,36,10],[85,8,88,8],[123,10,124,10],[113,10,116,10],[113,3,116,3],[113,8,116,8],[117,1,120,1],[121,0,130,0],[129,1,130,1],[129,2,130,2],[129,3,130,3],[129,8,130,8],[129,10,130,10],[121,1,122,1],[121,2,122,2],[121,3,122,3],[121,8,122,8],[121,10,122,10],[117,3,120,3],[117,8,120,8],[117,10,120,10],[136,8,137,8],[136,3,137,3],[136,10,137,10],[125,1,126,1],[125,2,126,2],[125,3,126,3],[125,8,126,8],[125,10,126,10],[127,3,128,3],[127,1,128,1],[127,2,128,2],[127,8,128,8],[127,10,128,10],[175,3,176,3],[175,8,176,8],[175,10,176,10],[177,3,178,3],[177,8,178,8],[177,10,178,10],[179,3,180,3],[179,8,180,8],[179,10,180,10],[181,3,182,3],[181,8,182,8],[181,10,182,10],[183,3,184,3],[183,10,184,10],[185,3,186,3],[185,10,186,10],[187,3,188,3],[187,10,188,10],[187,8,188,8],[185,8,186,8],[183,8,184,8],[208,3,209,3],[208,8,209,8],[208,10,209,10],[210,1,211,1],[210,2,211,2],[210,3,211,3],[210,8,211,8],[210,10,211,10],[216,3,217,3],[216,10,217,10],[216,8,217,8],[218,3,219,3],[218,8,219,8],[218,10,219,10],[212,1,213,1],[212,2,213,2],[212,3,213,3],[212,8,213,8],[212,10,213,10],[214,1,215,1],[214,2,215,2],[214,3,215,3],[214,10,215,10],[214,8,215,8],[226,3,227,3],[228,3,229,3],[224,10,225,10],[226,10,227,10],[228,10,229,10],[230,10,231,10],[230,3,231,3],[208,0,233,0],[232,1,233,1],[232,2,233,2],[232,3,233,3],[232,8,233,8],[232,10,233,10],[220,1,221,1],[220,2,221,2],[220,3,221,3],[220,8,221,8],[220,10,221,10],[222,3,223,3],[222,8,223,8],[222,10,223,10],[224,3,225,3],[216,1,217,1],[216,2,217,2]]}
[null,"Supplementary Table S6 - Explanation of characterized SNPs"]
["TF","refSNP ","HGVS Name (GRCh38.p2)","Gene"," Change in binding site sequence","iPWM","Change in information content ƚ","Prediction based on iPWMs","Experimental observation on the effect of the variant in literature","Comparison *","Reference"]
["AP2A","rs11568817","NC_000006.12:g.77463665A>C","Human HTR1B","CCCAGGTC → CCCAGGGC\nGACCTGGG → GCCCTGGG","HeLa-S3, USC, Bipartite","(-7.63223 bits) → 7.94436 bits\n(-6.71622 bits) → 8.86037 bits","The information content of the binding site becomes positive, so a new AP2 binding site is created. ","EMSA demonstrated that the G allele creates a new AP2 binding site.","Concordant","Duan et al. Polymorphisms in the 5'-untranslated region of the human serotonin receptor 1B (HTR1B) gene affect gene expression. 2003"]
[null,"rs5746092","NC_000006.12:g.159693279G>C","Human SOD2"," GCGGGGAGC → GCCGGGAGC","HeLa-S3, USC, Bipartite","(-9.03303 bits) → 6.54356 bits","The information content of the binding site becomes positive, so a new AP2 binding site is created. ","EMSA and antibody experiments showed that the mutation created a binding site of AP2 and a binding site of SP1.","Concordant","Xu et al. Mutations in the SOD2 Promoter Reveal a Molecular Basis for an AP-2-Dependent Dysregulation of MnSOD Expression in Cancer Cells. 2008"]
[null,"rs25531","NC_000017.11:g.30237328T>C","Human SLC6A4","CCCCCAGC → CCCCCGGC/GCCGGGGG","HeLa-S3, USC, Bipartite","2.86477 bits → 7.94436 bits / 8.86037 bits","The information content of the binding site increases by 5.07959 / 5.9956 bits, so AP2 binding increases by 25.07959 / 25.9956 ≈ 33.81 / 63.81 folds.","EMSA demonstrated that this protein–DNA interaction was quantitatively greater in the less common G allele oligonucleotide than that seen with major A allele oligonucleotides but less than that of consensus AP-2\noligonucleotides.","Concordant","Kraft et al. Sequence Analysis of the Serotonin Transporter and Associations with Antidepressant Response. 2005"]
[null,"rs41261045","NC_000022.11:g.25564658G>A","Human GRK3","① CCCCGAGGG → CCCCGAGGA, or\nCCCTCGGGG → TCCTCGGGG\n② CCCGAGGGG → CCCGAGGAG, or\nCCCCTCGGG → CTCCTCGGG","HeLa-S3, USC, Bipartite","① 5.43882 bits → -7.288179 bits\n5.43882 bits → -6.46945 bits\n② 5.43882 bits → -10.13777 bits\n5.43882 bits → -10.13777 bits","The information content of the binding site becomes negative, so AP2 binding is abolished.  ","EMSA and competition experiments showed that the A allele prevented AP2 binding.","Concordant","Zhou et al. Promoter Variant in the GRK3 Gene Associated with Bipolar Disorder Alters Gene Expression. 2008"]
["AP2C","rs11568817","NC_000006.12:g.77463665A>C","Human HTR1B","CCCAGGTC → CCCAGGGC\nGACCTGGG → GCCCTGGG","HeLa-S3, USC, Bipartite","(-8.06946 bits) → 7.92459 bits\n(-7.10011 bits) → 8.89394 bits","The information content of the binding site becomes positive, so a new AP2 binding site is created. ","EMSA demonstrated that the G allele creates a new AP2 binding site.","Concordant","Duan et al. Polymorphisms in the 5'-untranslated region of the human serotonin receptor 1B (HTR1B) gene affect gene expression. 2003"]
[null,"rs5746092","NC_000006.12:g.159693279G>C","Human SOD2"," GCGGGGAGC → GCCGGGAGC","HeLa-S3, USC, Bipartite","(-9.23513 bits) → 6.75892 bits","The information content of the binding site becomes positive, so a new AP2 binding site is created. ","EMSA and antibody experiments showed that the mutation created a binding site of AP2 and SP1.","Concordant","Xu et al. Mutations in the SOD2 Promoter Reveal a Molecular Basis for an AP-2-Dependent Dysregulation of MnSOD Expression in Cancer Cells. 2008"]
[null,"rs25531","NC_000017.11:g.30237328T>C","Human SLC6A4","CCCCCAGC → CCCCCGGC/GCCGGGGG","HeLa-S3, USC, Bipartite","3.07309 bits → 7.92459 bits / 8.89394 bits","The information content of the binding site increases by 4.8515 / 5.82085 bits, so AP2 binding increases by 24.8515 / 25.82085 ≈ 28.87 / 56.53 folds.","EMSA demonstrated that this protein–DNA interaction was quantitatively greater in the less common G allele oligonucleotide than that seen with major A allele oligonucleotides but less than that of consensus AP-2\noligonucleotides.","Concordant","Kraft et al. Sequence Analysis of the Serotonin Transporter and Associations with Antidepressant Response. 2005"]
[null,"rs41261045","NC_000022.11:g.25564658G>A","Human GRK3","① CCCCGAGGG → CCCCGAGGA, or\nCCCTCGGGG → TCCTCGGGG\n② CCCGAGGGG → CCCGAGGAG, or\nCCCCTCGGG → CTCCTCGGG","HeLa-S3, USC, Bipartite","① 5.46535 bits → -7.718877 bits\n5.46535 bits → -6.85388 bits\n② 5.46535 bits → -10.5287 bits\n5.46535 bits → -10.5287 bits","The information content of the binding site becomes negative, so AP2 binding is abolished.  ","EMSA and competition experiments showed that the A allele prevented AP2 binding.","Concordant","Zhou et al. Promoter Variant in the GRK3 Gene Associated with Bipolar Disorder Alters Gene Expression. 2008"]
["AP4","rs2287839","NC_000019.10:g.9830138C>G","Human PIN1","CAGCTGTC → GAGCTGTC","HepG2, HAIB","11.1118 bits → 8.02718 bits","The information content of the binding site decreases by 3.08462 bits, so CEBPB binding decreases by 23.08462 ≈ 8.48 folds.","EMSA showed that the wild-type allele formed strong complexes with AP4 while the variant showed 75% (p=0.017) reduction of binding to AP4.","Concordant","Ma et al. A Functional Polymorphism in PIN1 that Prevents its Suppression by AP4 Is Associated with Delayed Onset of Alzheimer’s disease. 2013"]
["CEBPB","rs4553808","NC_000002.12:g.203866282A>G","Human CTLA4","TTTTTAAAAA → TTTTCAAAAA","IMR90, Stanford","(-14.63798 bits) → 2.8757 bits","The information content of the binding site becomes positive, so a new CEBPB binding site is created. ","PCR-based chromatin immunoprecipitation showed that CEBPB can bind only when the G allele is present.","Concordant","Wang et al. Two SNPs in the promoter region of the CTLA-4 gene affect binding of transcription factors and are associated with human myasthenia gravis. 2008"]
[null,"rs66841827","NC_000001.11:g.94542967_94542984del18","Human F3","CTTACTGAAC → TATACTGAAC","IMR90, Stanford","2.56574 bits → -17.204781 bits","The information content of the binding site becomes negative, so CEBPB binding is abolished.  ","EMSA, competition and antibody experiments demonstrated that the 18bp insertion created a CEBP binding site.","Concordant","Terry et al. Polymorphisms in the 5'-UTR of the tissue factor gene are associated with altered expression in human endothelial cells. 2004"]
[null,"rs34223104","NC_000019.10:g.40991224T>C","Human CYP2B6","ATTTTATAAC → ATTTCATAAC","IMR90, Stanford","(-4.93208 bits) → 12.5816 bits","The information content of the binding site becomes positive, so a new CEBPB binding site is created.","EMSA demonstrated that the mutation creates a new CEBP binding site.","Concordant","Zukunft et al. A Natural CYP2B6 TATA Box Polymorphism (-82T→C) Leading to Enhanced Transcription and Relocation of the Transcriptional Start Site. 2005"]
[null,"N/A","NC_001802.1:g.8971C>T","HIV1 LTR","  CTTGCTACAA → TTTGCTACAA","IMR90, Stanford","3.86106 bits → 1.59833 bits","The information content of the binding site decreases by 2.26273 bits, so CEBPB binding decreases by 22.26273 ≈ 4.80 folds.","EMSA showed that the T allele is a lower-affinity binding site.","Concordant","Shah et al. Functional properties of the HIV-1 long terminal repeat containing single-nucleotide polymorphisms in Sp site III and CCAAT/enhancer binding protein site I. 2014"]
[null,"N/A","NC_000023.11:g.139530748A>G","Human F9","CTTTCACAAT → CTTTCACAGT","IMR90, Stanford","11.4183 bits → 3.98399 bits","The information content of the binding site decreases by 7.43431 bits, so CEBPB binding decreases by 27.43431 ≈ 172.96 folds.","Competiton experiments showed that the G allele competed out the footprint roughly 100 times less efficiently than the normal A allele.","Concordant","Crossley et al. Disruption of a CEBP binding site in the factor IX promoter is associated with haemophilia B. 1990"]
[null,"rs763110","NC_000001.11:g.172658358C>T","Human FASL","ATTTCGCAAT/ATTGCGAAAT → ATTTCACAAT","IMR90, Stanford","11.7237/11.5148 bits → 13.5745 bits","The information content of the binding site increases by 1.8508/2.0597 bits, so CEBPB binding increases by 21.8508 or 22.0597 ≈ 3.61 or 4.17 folds.","EMSA, competition and supershift experiments demonstrated that labeled probe with T allele bound but appeared to have much lower affinity for the transcription factor CEBPB than that of the C allele.","Discordant","Wu et al. A Novel Polymorphic CAAT/Enhancer-Binding Protein Element in the FasL Gene Promoter Alters Fas Ligand Expression: A Candidate Background Gene in African American Systemic Lupus Erythematosus Patients. 2003"]
["ELF1","rs2227631","NC_000007.14:g.101126257A>G","Human PAI1","GAAGAAGTGAA → GAGGAAGTGAA","K562, HAIB","(-3.94526 bits) → 12.2296 bits","The information content of the binding site becomes positive, so a new ELF1 binding site is created.","EMSA and supershift experiments identified specific binding of ELF1 to the G allele.","Concordant","Hultman et al. Allele-specific transcription of the PAI-1 gene in human astrocytes. 2010"]
[null,null,null,null,"TCACTTCTTCG → TCACTTCCTCG","HepG2, HAIB","2.53792 bits → 12.5515 bits","The information content of the binding site increases by 10.01358 bits, so ELF1 binding increases by 210.01358 ≈ 1033.68 folds.",null,"Qualitatively concordant, quantitatively discordant"]
["ELK1","rs968567","NC_000011.10:g.61828092C>T","Human FADS2","CCGGGAGCTCA → CCGGAAGCTCA","K562, Stanford","7.57102 bits → 11.368 bits","The information content of the binding site increases by 3.79698 bits, so ELK1 binding increases by 23.79698 ≈ 13.90 folds.","EMSA and competition experiments showed that the T allele is a stronger binding site than the C allele.","Concordant","Lattka et al. A common FADS2 promoter polymorphism increases promoter activity and facilitates binding of transcription factor ELK1. 2009"]
[null,null,null,null,"GAGCTCCCGGG → GAGCTTCCGGG","HeLa-S3, Stanford","7.73004 bits → 11.7755 bits","The information content of the binding site increases by 4.04546 bits, so ELK1 binding increases by 24.04546 ≈ 16.51 folds.",null,"Concordant"]
[null,"rs2227631","NC_000007.14:g.101126257A>G","Human PAI1","GAAGAAGTGAA → GAGGAAGTGAA","K562, Stanford","5.3038 bits → 10.7949 bits","The information content of the binding site increases by 5.4911 bits, so ELK1 binding increases by 25.4911 ≈ 44.98 folds.","EMSA and supershift experiments identified specific binding of ELK1 to the G allele.","Qualitatively concordant, quantitatively discordant","Hultman et al. Allele-specific transcription of the PAI-1 gene in human astrocytes. 2010"]
[null,null,null,null," TCACTTCTTCG → TCACTTCCTCG","HeLa-S3, Stanford","(-2.41943 bits) → 10.9604 bits","The information content of the binding site becomes positive, so a new ELK1 binding site is created.",null,"Concordant"]
["ELK4","rs554219","NC_000011.10:g.69516874C>G","Human CCND1","GGGTTTCCGGT → GGGTTTCCCGT","HeLa-S3, USC","10.937 bits → 4.0507 bits","The information content of the binding site decreases by 6.8863 bits, so ELK4 binding decreases by 26.8863 ≈ 118.30 folds.","EMSA and ChIP assays showed that the common C allele shows a 7.7-fold enrichment over a negative control and a 7.1- fold enrichment over the risk G allele.","Concordant","French et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. 2013"]
[null,null,null,null,"ACCGGAAACCC → ACGGGAAACCC","HEK293, USC","10.3132 bits → 2.40925 bits","The information content of the binding site decreases by 7.90395 bits, so ELK4 binding decreases by 27.90395 ≈ 239.51 folds.",null,"Concordant"]
[null,"rs72656914","NC_000001.11:g.150579726C>T","Human MCL1","CAGCTTCCGGA → CAGCTTCTGGA","HeLa-S3, USC","11.3231 bits → -0.74652 bit","The information content of the binding site becomes negative, so ELK4 binding is abolished. ","EMSA and supershift experiments demonstrated that the complex on the T allele was only weakly detected on the U118 cell line, and was not detected on the other three cell lines.","Concordant","Day et al. ELK4 neutralization sensitizes glioblastoma to apoptosis through downregulation of the anti-apoptotic protein Mcl-1. 2011"]
[null,null,null,null,"TCCGGAAGCTG → TCCAGAAGCTG","HEK293, USC","11.2211 bits → 6.54984 bits","The information content of the binding site decreases by 4.67126 bits, so ELK4 binding decreases by 24.67126 ≈ 25.48 folds.",null,"Concordant"]
["ESR1","rs5050","NC_000001.11:g.230714140T>G","Human AGT","AGGGCATCGTGACCC → AGGGCCTCGTGACCC\n                                   → GGGCCTCGTGACCC\nGGGTCACGATGCCCT → GGGTCACGAGGCCCT\n                                   → GGGTCACGAGGCCC","T47D, HAIB, Bisphenol","16.1726 bits → 3.11171 bits\n                      → 10.3902 bits\n15.9574 bits → 2.91144 bits\n                      → 10.6085 bits","The information content of the binding site decreases by 13.06089/5.7824 or 13.04596/5.3489 bits, so ESR binding decreases by 213.06089/25.7824 or 213.04596/25.3489 ≈ 8545.15/55.04 or 8457.17/40.75 folds.","EMSA and cotranscfection showed that the mutant G allele decreased ESR1 binding and estrogen-induced promoter activity.","Concordant","Zhao et al. Role of C/A Polymorphism at -20 on the Expression of Human Angiotensinogen Gene. 1999\nMorgan et al. Polymorphism in oestrogen response element associated with variation in plasma angiotensinogen concentrations in healthy pregnant women. 2000"]
[null,"rs378815","NC_000023.11:g.139530038T>C","Human F9","AAATGAAGTTTGACTT → AAATGAAGTTTGACCT","T47D, HAIB, Bisphenol","3.67828 bits → 5.72803 bits","The information content of the binding site increases by 2.04975 bits, so ESR1 binding increases by 22.04975 ≈ 4.14 folds.","EMSA demonstrated that the C allele has a higher affinity for ESR1 than the T allele.","Concordant","Adams et al. Identification and functional characterization of a polymorphic oestrogen response element in the human coagulation factor IX gene promoter. 2007"]
[null,"rs2333227","NC_000017.11:g.58281401C>T","Human MPO","GAGGCGGGTGGATC → GAGGCAGGTGGATC\nGATCCACCCGCCTC → GATCCACCTGCCTC","T47D, HAIB, Bisphenol","(-2.60252 bits) → 3.63817 bits\n(-0.95589 bit) → 4.64433 bits","The information content of the binding site becomes positive, so a new ESR1 binding site is created. ","EMSA demonstrated that ESR1 bound exclusively to the T allele.","Concordant","Kumar et al. Peroxisome Proliferator-activated Receptor Ligands Regulate Myeloperoxidase Expression in Macrophages by an Estrogen-dependent Mechanism Involving the 463GA Promoter Polymorphism. 2003"]
["FOXA1","rs4784227","NC_000016.10:g.52565276C>T","Human TOX3","TGTTTGCCGAT → TGTTTGCTGAT","T47D, HAIB, Replicate 2","10.3918 bits → 11.925837 bits","The information content of the binding site increases by 1.534037 bits, so FOXA1 binding increases by 21.534037 ≈ 2.90 folds.","ChIP-assays confirmed that FOXA1 is preferentially recruited to the T allele.","Concordant","Cowper-Sal·lari et al. Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. 2012"]
[null,"rs11986220","NC_000008.11:g.127519444A>T","Human 8q24","TATTTATTTTT → TATTTAATTTT","T47D, HAIB, Replicate 2","10.859 bits → -4.290007 bits","The information content of the binding site becomes negative, so FOXA1 binding is abolished. ","EMSA showed that the normal allele is stronger than the mutant allele and competed better than the mutant allele for FoxA1 binding to a consensus Fox oligonucleotide.","Qualitatively concordant, quantitatively discordant","Jia et al. Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus. 2009"]
[null,"rs59678213","NC_000004.12:g.68568639T>C","Human UGT2B17","TATTTACAATT → TATTCACAATT","T47D, HAIB, Replicate 2","9.46136 bits → -7.58309 bits","The information content of the binding site becomes negative, so FOXA1 binding is abolished. ","EMSA showed that FOXA1 can bind to both alleles, but the T allele is much stronger than the C allele. However, The iPWM predicted three other binding sites in the oligo used by the paper. These sites are not affected by the SNP and explain why FOXA1 binding to the oligo was still observed when the C allele is present.","Concordant","Hu et al. A novel polymorphism in a forkhead box A1 (FOXA1) binding site of the human UDP glucuronosyltransferase 2B17 gene modulates promoter activity and is associated with altered levels of circulating androstane-3α,17β-diol glucuronide. 2010"]
["FOXA2","N/A","N/A (Artificially introduced mutations)","Human FGB","TATTTACTTGT → GAAGTACTTGT","GM12878, HAIB","10.6379 bits → -18.04716 bits","The information content of the binding site becomes negative, so FOXA2 binding is abolished. ","EMSA showed that the mutation abolished the binding site.","Concordant","Verschuur et al. A Hepatocyte Nuclear Factor-3 Site in the Fibrinogen β Promoter Is Important for Interleukin 6-induced Expression, and Its Activity Is\nInfluenced by the Adjacent -148C/T Polymorphism. 2005"]
[null," rs573225","NC_000002.12:g.168901031G>A","Human G6PC2 ","TGTTTGCTTGA → TGTTTGTTTGA","GM12878, HAIB","10.8545 bits → 9.1048 bits","The information content of the binding site decreases by 1.7497 bits, so FOXA2 binding decreases by 21.7497 ≈ 3.36 folds.","EMSA and supershift showed that the G allele is a binding site for FOXA2, whereas the A allele cannot bind to FOXA2.","Qualitatively concordant, quantitatively discordant","Dos Santos et al. A Single-Nucleotide Polymorphism in a Methylatable Foxa2 Binding Site of the G6PC2 Promoter Is Associated With Insulin Secretion In Vivo and Increased Promoter Activity In Vitro. 2008"]
["GATA1","rs35324967","NC_000011.10:g.5232765C>T","Human delta-globin","CCCTATCTG → CCTTATCTG","K562, USC","10.7047 bits → 14.1071 bits","The information content of the binding site increases by 3.4024 bits, so GATA1 binding increases by 23.4024 ≈ 10.57 folds.","Gel-retardation assay has shown that the T allele has a higher affinity than the C allele.","Concordant","Moi et al. Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3' to the delta-globin gene. 1992"]
[null,null,null,null,"CAGATAGGG → CAGATAAGG","FetalPBDE, USC","8.86422 bits → 13.5176 bits","The information content of the binding site increases by 4.65338 bits, so GATA1 binding decreases by 24.65338 ≈ 25.17 folds.",null,"Discordant"]
[null,"rs35476703","NC_000020.11:g.45174234C>G","Human PI3","ATGTATCAT → ATCTATCAT","K562, USC","(-2.2284 bits) → 1.99977 bits","The information content of the binding site becomes positive, so a new GATA1 binding site is created. ","EMSA, competiton and supershift experiments demonstrated that GATA1 binds to the G-allele of the -689C>G polymorphism in the promoter region of PI3 gene.","Concordant","Chowdhury et al. Identification of novel functional sequence variants in the gene for peptidase inhibitor 3. 2006"]
[null,null,null,null,"ATGATACAT → ATGATAGAT","FetalPBDE, USC","(-1.65001 bits) → 1.96789 bits","The information content of the binding site becomes positive, so a new GATA1 binding site is created. ",null,"Concordant"]
[null,"rs2251746","NC_000001.11:g.159302270T>C","Human FCER1A","CTGTATCAT → CTGTGTCAT","K562, USC","0.898983 bit → -12.422287 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ","EMSA demonstrated that the T allele is a true weak binding site, while the C allele is not.","Concordant","Hasegawa et al. A Novel  66T/C Polymorphism in FceRI alpha-Chain Promoter Affecting the Transcription Activity: Possible Relationship to Allergic Diseases. 2003"]
[null,null,null,null,"ATGATACAG → ATGACACAG","FetalPBDE, USC","1.47032 bits → -7.57121 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Concordant"]
[null,"rs4516035","NC_000012.12:g.47906043T>C","Human VDR","CAATATCTT → CAATGTCTT","K562, USC","2.07594 bits → -11.24533 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ","EMSA demonstrated that the T allele is a binding site, whereas the C allele is unable to compete for GATA binding to the T allele.","Concordant","Fang et al. Promoter and 3′-Untranslated-Region Haplotypes in the Vitamin D Receptor Gene Predispose to Osteoporotic Fracture: The Rotterdam Study. 2005\nHalsall et al. The unfavorable effect of the A allele of the vitamin D receptor promoter polymorphism A-1012G has different mechanisms related to susceptibility and outcome of malignant melanoma. 2009 "]
[null,null,null,null,"AAGATATTG → AAGACATTG","FetalPBDE, USC","4.26672 bits → -4.77481 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Concordant"]
[null,"N/A","NC_000016.10:g.159710T>C","Human alpha-globin genes","CATTATTAG → CATTATCAG","K562, USC","(-5.00202) bits → 8.39467 bits","The information content of the binding site becomes positive, so a new GATA1 binding site is created. ","EMSA and supershifts demonstrated that the mutation created a GATA1 binding site.","Concordant","Gobbi et al. A Regulatory SNP Causes a Human Genetic Disease by Creating a New Transcriptional Promoter. 2006"]
[null,null,null,null,"CTAATAATG → CTGATAATG","FetalPBDE, USC","0.333421 bit → 8.13968 bits","The information content of the binding site increases by 7.806259 bits, so GATA1 binding increases by 27.806259 ≈ 223.83 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,"N/A","NC_000009.12:g.132978582A>G","Human GFI1B","GCTTATCAA → GCTCATCAA","K562, USC","9.28425 bits → 4.10376 bits","The information content of the binding site decreases by 5.18049 bits, so GATA1 binding decreases by 25.18049 ≈ 36.26 folds.","EMSA and supershifts demonstrated that the mutation decreases GATA1 binding.","Concordant","Hernández et al. Human promoter mutations unveil Oct-1 and GATA-1 opposite action on Gfi1b regulation. 2010"]
[null,null,null,null,"TTGATAAGC → TTGATGAGC","FetalPBDE, USC","9.11108 bits → -4.03885 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Qualitatively concordant, quantitatively discordant"]
[null,"rs34975911","NC_000011.10:g.5234560A>G","Human delta-globin","GCTTATCTT → GCTCATCTT","K562, USC","11.4655 bits → 6.285 bits","The information content of the binding site decreases by 5.1805 bits, so GATA1 binding decreases by 25.1805 ≈ 36.26 folds.","EMSA demonstrated that the mutant allele is a weaker binding site than the wild-type allele.","Concordant","Matsuda et al. δ-Thalassemia Caused by Disruption of the Site for an Erythroid-Specific Transcription Factor, GATA-1, in the δ-Globin Gene Promoter. 1992"]
[null,null,null,null,"AAGATAAGC → AAGATGAGC","FetalPBDE, USC","11.9136 bits → -1.23633 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Qualitatively concordant, quantitatively discordant"]
[null,"rs1341239","NC_000006.12:g.22303975A>C","Human prolactin","AATTATCTT → AATTCTCTT","K562, USC","5.04074 bits → 0.4865 bit","The information content of the binding site decreases by 4.55424 bits, so GATA1 binding decreases by 24.55424 ≈ 23.49 folds.","EMSA demonstrated that the GATA-related proteins are involved in binding to each allele and the A allele is stronger.","Concordant","Stevens et al. Characterization of a Prolactin Gene Polymorphism and Its Associations With Systemic Lupus Erythematosus. 2001"]
[null,null,null,null,"AAGATAATT → AAGAGAATT","FetalPBDE, USC","5.95504 bits → -1.31309 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Qualitatively concordant, quantitatively discordant"]
[null,"rs2814778","NC_000001.11:g.159204893T>C","Human DARC","TCTTATCTT → TCTTACCTT","K562, USC","12.2326 bits → 2.00294 bits","The information content of the binding site decreases by 10.22966 bits, so GATA1 binding decreases by 210.22966 ≈ 1200.70 folds.","EMSA showed that the mutation abolished GATA1 binding.","Qualitatively concordant, quantitatively discordant","Tournamille et al. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. 1995"]
[null,null,null,null,"AAGATAAGA → AAGGTAAGA","FetalPBDE, USC","13.0663 bits → -0.1038 bit","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Concordant"]
[null,"rs730882059","NC_000022.11:g.19723410C>G","Human GP1BB","TGCTATCTG → TGCTATGTG","K562, USC","8.39079 bits → 0.038452 bit","The information content of the binding site decreases by 8.352338 bits, so GATA1 binding decreases by 28.352338 ≈ 326.82 folds.","EMSA showed that the GATA-1 protein is binding to the normal GATA consensus site, but is unable to bind to the mutated GATA site.","Qualitatively concordant, quantitatively discordant","Ludlow et al. Identification of a Mutation in a GATA Binding Site of the Platelet Glycoprotein Ibb Promoter Resulting in the Bernard-Soulier Syndrome. 1996"]
[null,null,null,null,"CAGATAGCA → CACATAGCA","FetalPBDE, USC","6.50135 bits → -6.66248 bits","The information content of the binding site becomes negative, so GATA1 binding is abolished. ",null,"Concordant"]
[null,"rs2107538","NC_000017.11:g.35880776C>T","Human RANTES","TCTTACCTCA → TCTTATCTCA","K562, USC","3.30105 bits → 13.5307 bits","The information content of the binding site increases by 10.22965 bits, so GATA1 binding increases by 210.22965 ≈ 1200.69 folds.","EMSA demonstrated that the complex caused by GATA1 binding formed exclusively with the mutant T allele.","Qualitatively concordant, quantitatively discordant","Nickel et al. Atopic Dermatitis Is Associated with a Functional Mutation in the Promoter of the C-C Chemokine RANTES. 2000"]
[null,null,null,null,"GAGGTAAGA → GAGATAAGA","FetalPBDE, USC","0.360508 bit → 13.5306 bits","The information content of the binding site increases by 13.170092 bits, so GATA1 binding increases by 213.170092 ≈ 9217.07 folds.",null,"Qualitatively concordant, quantitatively discordant"]
["GATA2"," rs7649970","NC_000003.12:g.12350773C>T","Human PPARG","ACGATAAGT → ACAATAAGT","K562, HAIB","3.99572 bits → -11.65098 bits","The information content of the binding site becomes negative, so GATA2 binding is abolished. ","EMSA showed that GATA2 could bind weakly to the wild-type GATA binding site but not to the mutated site. ","Concordant","Meirhaeghe et al. Study of a new PPARgamma2 promoter polymorphism and haplotype analysis in a French population. 2005"]
[null,null,null,null,"ACGATAAGT → ACAATAAGT","K562, USC","3.41991 bits → -11.3708 bits","The information content of the binding site becomes negative, so GATA2 binding is abolished. ",null,"Concordant"]
[null,"rs35324967","NC_000011.10:g.5232765C>T","Human delta-globin","CAGATAGGG → CAGATAAGG","K562, HAIB","10.0097 bits → 13.1203 bits","The information content of the binding site increases by 3.1106 bits, so GATA2 binding increases by 23.1106 ≈ 8.64 folds.","Gel-retardation assay has shown that the mutant allele has a higher affinity than the wild-type allele.","Concordant","Moi et al. Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3' to the delta-globin gene. 1992"]
[null,null,null,null,"CAGATAGGG → CAGATAAGG","K562, USC","10.5188 bits → 13.5833 bits","The information content of the binding site increases by 3.0645 bits, so GATA2 binding increases by 23.0645 ≈ 8.37 folds.",null,"Concordant"]
[null,"rs4516035","NC_000012.12:g.47906043T>C","Human VDR","AAGATATTG → AAGACATTG","K562, HAIB","4.40856 bits → -5.81551 bits","The information content of the binding site becomes negative, so GATA2 binding is abolished. ","EMSA demonstrated that the T allele is a binding site, whereas the C allele is unable to compete for GATA binding to the T allele.","Concordant","Fang et al. Promoter and 3′-Untranslated-Region Haplotypes in the Vitamin D Receptor Gene Predispose to Osteoporotic Fracture: The Rotterdam Study. 2005\nHalsall et al. The unfavorable effect of the A allele of the vitamin D receptor promoter polymorphism A-1012G has different mechanisms related to susceptibility and outcome of malignant melanoma. 2009 "]
[null,null,null,null,"AAGATATTG → AAGACATTG","K562, USC","2.91597 bits → -11.76492 bits","The information content of the binding site becomes negative, so GATA2 binding is abolished. ",null,"Concordant"]
[null,"rs2107538","NC_000017.11:g.35880776C>T","Human RANTES","GAGGTAAGA → GAGATAAGA","K562, HAIB","2.5775 bits → 13.4331 bits","The information content of the binding site increases by 10.8556 bits, so GATA2 binding increases by 210.8556 ≈ 1892.54 folds.","EMSA demonstrated that the complex caused by GATA2 binding formed exclusively with the mutant T allele.","Qualitatively concordant, quantitatively discordant","Nickel et al. Atopic Dermatitis Is Associated with a Functional Mutation in the Promoter of the C-C Chemokine RANTES. 2000"]
[null,null,null,null,"GAGGTAAGA → GAGATAAGA","K562, USC","(-1.18504 bits) → 13.6058 bits","The information content of the binding site becomes positive, so a new GATA2 binding site is created. ",null,"Concordant"]
[null,"rs1341239","NC_000006.12:g.22303975A>C","Human prolactin","AAGATAATT → AAGAGAATT","K562, HAIB","7.37142 bits → 2.90766 bits","The information content of the binding site decreases by 4.46376 bits, so GATA2 binding decreases by 24.46376 ≈ 22.07 folds.","EMSA demonstrated that the GATA-related proteins are involved in binding to each allele and the A allele is stronger.","Concordant","Stevens et al. Characterization of a Prolactin Gene Polymorphism and Its Associations With Systemic Lupus Erythematosus. 2001"]
[null,null,null,null,"AAGATAATT → AAGAGAATT","K562, USC","5.94033 bits → 2.28254 bits","The information content of the binding site decreases by 3.65779 bits, so GATA2 binding decreases by 23.65779 ≈ 12.62 folds.",null,"Concordant"]
["GATA3","rs361072","NC_000003.12:g.138759702G>A","Human PIK3CB","AGATATTT → AAATATTT","SHSY5Y, USC","0.84709 bit → -10.24345 bits","The information content of the binding site becomes negative, so GATA3 binding is abolished. ","EMSA showed that GATA3 specifically binds to the G allele.","Concordant","Stunff et al. Association analysis indicates that a variant GATA-binding site in the PIK3CB promoter is a Cis-acting expression quantitative trait locus for this gene and attenuates insulin resistance in obese children. 2008"]
[null,"rs35324967","NC_000011.10:g.5232765C>T","Human delta-globin","CAGATAGG → CAGATAAG","SHSY5Y, USC","7.56281 bits → 11.6866 bits","The information content of the binding site increases by 4.12379 bits, so GATA3 binding increases by 24.12379 ≈ 17.43 folds.","Gel-retardation assay has shown that the T allele has a higher affinity than the C allele.","Concordant","Moi et al. Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3' to the delta-globin gene. 1992"]
[null,"rs2107538","NC_000017.11:g.35880776C>T","Human RANTES","AGGTAAGA → AGATAAGA","SHSY5Y, USC","0.196564 bit → 13.162 bits","The information content of the binding site increases by 12.965436 bits, so GATA3 binding increases by 212.965436 ≈ 7998.07 folds.","EMSA demonstrated that the complex caused by GATA3 binding formed exclusively with the mutant T probe.","Qualitatively concordant, quantitatively discordant","Nickel et al. Atopic Dermatitis Is Associated with a Functional Mutation in the Promoter of the C-C Chemokine RANTES. 2000"]
[null,"rs4516035","NC_000012.12:g.47906043T>C","Human VDR","AGATATTG → AGACATTG","SHSY5Y, USC","2.91597 bits → -7.83489 bits","The information content of the binding site becomes negative, so GATA3 binding is abolished. ","EMSA demonstrated that the T allele is a binding site, whereas the C allele is unable to compete for GATA binding to the T allele.","Concordant","Fang et al. Promoter and 3′-Untranslated-Region Haplotypes in the Vitamin D Receptor Gene Predispose to Osteoporotic Fracture: The Rotterdam Study. 2005\nHalsall et al. The unfavorable effect of the A allele of the vitamin D receptor promoter polymorphism A-1012G has different mechanisms related to susceptibility and outcome of malignant melanoma. 2009 "]
["GR/NR3C1","rs77186188","NC_000006.12:g.118548260A>C","Human PLN","AGAACACTTTTTCTC → AGCACACTTTTTCTC","A549, HAIB, 50nM Dexamethasone for 1 hour","9.87085 bits → 9.95503 bits","The information content of the binding site increases by 0.08418 bit, so GR binding increases by 20.08418 ≈ 1.06 folds.","EMSA demonstrated that the mutation enhances binding.","Concordant","Haghighi et al. A Human Phospholamban Promoter Polymorphism in Dilated Cardiomyopathy Alters Transcriptional Regulation by Glucocorticoids. 2008"]
[null,"rs2794521","NC_000001.11:g.159715306C>T","Human CRP","AACACCGCGTGTTCT → AACACCGCATGTTCT","A549, HAIB, 50nM Dexamethasone for 1 hour","9.46971 bits → 8.87163 bits","The information content of the binding site decreases by 0.59808 bit, so GR binding decreases by 20.59808 ≈ 1.51 folds.","EMSA demonstrated that the C allele is a stronger binding site than the T allele.","Concordant","Wang et al. Functional analysis of the C-reactive protein (CRP) gene -717A>G polymorphism associated with coronary heart disease. 2008"]
["IRF1","rs1024611","NC_000017.11:g.34252769A>G","Human CCL2","AGCTATCACTTTC → AGCTGTCACTTTC","K562, Stanford\nIFNa for 30 minutes","8.26693 bits → 10.2585 bits","The information content of the binding site increases by 1.99157 bits, so IRF1 binding increases by 21.99157 ≈ 3.97 folds.","ChIP assays showed that for IRF1 the A allele is stronger than the G allele.","Discordant","Page et al. Regulation of CCL2 expression by an upstream TALE homeodomain protein-binding site that synergizes with the site created by the A-2578G SNP. 2011"]
["JUND","rs1997794","NC_000020.11:g.1994212T>C","Human PDYN","TGACACA → CGACACA\nTGTGTCA → TGTGTCG","HeLa-S3, Stanford","6.49756 bits → -9.79541 bits\n5.91558 bits → -10.37739 bits","The information content of the binding site becomes negative, so AP1 binding is abolished. ","EMSA and antibody supershift demonstrated that AP1 dimers containing JUND can bind to the normal allele, but not the mutant allele.","Concordant","Taqi et al. Prodynorphin promoter SNP associated with alcohol dependence forms noncanonical AP-1 binding site that may influence gene expression in human brain. 2011"]
["MEF2A","rs3812852","NC_000013.11:g.73057735A>G","Human KLF5","TTTTACATATACCA → TCTTACATATACCA","K562, HAIB","3.65603 bits → 2.01784 bits","The information content of the binding site decreases by 1.63819 bits, so MEF2A binding decreases by 21.63819 ≈ 3.11 folds.","In EMSA assays no complex caused by MEF2A binding appeared on the G allele, but in competition experiments a 100-fold excess of the G allele reduced the intensity of the band formed on the A allele.","Concordant","Oishi et al. Regulatory polymorphism in transcription factor KLF5 at the MEF2 element alters the response to angiotensin II and is associated with human hypertension. 2010"]
[null,null,null,null,"TTTTACATATACC  →  TCTTACATATACC","GM12878, HAIB","3.25009 bits → 0.775755 bit","The information content of the binding site decreases by 2.474335 bits, so MEF2A binding decreases by 22.474335 ≈ 5.56 folds.",null,"Concordant"]
[null,"rs9349379","NC_000006.12:g.12903725A>G","Human PHACTR1","AGCTATTTTTATA → AGCTACTTTTATA","GM12878, HAIB","14.5567 bits → 10.4926 bits","The information content of the binding site decreases by 4.0641 bits, so MEF2A binding decreases by 24.0641 ≈ 16.73 folds.","EMSA and antibody supershift demonstrated that the G allele is not a binding site.","Qualitatively concordant, quantitatively discordant","Beaudoin et al. Myocardial Infarction–Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries. 2015"]
[null,null,null,null,"AGCTATTTTTATAT → AGCTACTTTTATAT","K562, HAIB","13.8689 bits → 10.2759 bits","The information content of the binding site decreases by 3.593 bits, so MEF2A binding decreases by 23.593 ≈ 12.07 folds.",null,"Qualitatively concordant, quantitatively discordant"]
["MEF2C","rs9349379","NC_000006.12:g.12903725A>G","Human PHACTR1","TATAAAAATAGC → TATAAAAGTAGCT","GM12878, HAIB","14.1664 bits → 10.3162 bits","The information content of the binding site decreases by 3.8502 bits, so MEF2A binding decreases by 23.8502 ≈ 14.42 folds.","EMSA and antibody supershift demonstrated that the G allele is not a binding site.","Qualitatively concordant, quantitatively discordant","Beaudoin et al. Myocardial Infarction–Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries. 2015"]
["NFE2","rs4932178","NC_000015.10:g.90868426C>T","Human FURIN","TGCAGACCCACCC → TGCAGACTCACCC","K562, Yale","2.45085 bits → 9.126 bits","The information content of the binding site increases by 6.67515 bits, so NFE2 binding increases by 26.67515 ≈ 102.19 folds.","Site-directed mutagenesis was used to prove the SNP lies within NFE2 binding site, and the T allele results in more effective binding.","Concordant","Lei et al. Influence of a Single Nucleotide Polymorphism in the P1 Promoter of the Furin Gene on Transcription Activity and Hepatitis B Virus Infection. 2009"]
["NFKB","rs13102260","NC_000004.12:g.3074678G>A","Human HTT","GGGGCTGCCG → AGGGCTGCCG","GM12878, Stanford","2.70723 bits → -11.93244 bits","The information content of the binding site becomes negative, so NFKB binding is abolished. ","EMSA showed that the A allele fully abolishes NFKB binding.","Concordant","Becanovic et al. A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease. 2015"]
[null,null,null,null,"No predicted binding site","GM19099, Stanford","N/A","N/A",null,"Discordant"]
[null,null,null,null,"GGGGGCTGCC → GAGGGCTGCC","GM19193, Stanford","4.14858 bits → -9.52868 bits","The information content of the binding site becomes negative, so NFKB binding is abolished. ",null,"Concordant"]
[null,null,null,null,"GGGGGCTGCC → GAGGGCTGCC","GM12891, Stanford","7.26463 bits → -7.89367 bits","The information content of the binding site becomes negative, so NFKB binding is abolished. ",null,"Concordant"]
[null,"rs5743836","NC_000003.12:g.52226766A>G","Human TLR9","GGGAGTTTTC → GGGAGTTTCC","GM12878, Stanford","11.5452 bits → 13.3578 bits","The information content of the binding site increases by 1.8126 bits, so NFKB binding increases by 21.8126 ≈ 3.51 folds.","Noshift transcription factor analysis showed that the binding affinity of the variant G allele was significantly higher compared to the wild-type A A allele.","Concordant","Ng et al. Increase in NF-κB Binding Affinity of the Variant C Allele of the Toll-Like Receptor 9  1237T/C Polymorphism Is Associated with Helicobacter pylori-Induced Gastric Disease. 2010"]
[null,null,null,null,"GGGAGTTTTC → GGGAGTTTCC","GM19099, Stanford","10.7254 bits → 13.9142 bits","The information content of the binding site increases by 3.1888 bits, so NFKB binding increases by 23.1888 ≈ 9.12 folds.",null,"Concordant"]
[null,null,null,null,"GGGAGTTTTC → GGGAGTTTCC","GM19193, Stanford","10.5983 bits → 13.8961 bits","The information content of the binding site increases by 3.2978 bits, so NFKB binding increases by 23.2978 ≈ 9.83 folds.",null,"Concordant"]
[null,null,null,null,"GGGAGTTTTC → GGGAGTTTCC","GM12891, Stanford","11.1999 bits → 13.7949 bits","The information content of the binding site increases by 2.595 bits, so NFKB binding increases by 22.595 ≈ 6.04 folds.",null,"Concordant"]
[null,"rs324011","NC_000012.12:g.57108399C>T","Human STAT6","GGGACCGTCC → GGGACTGTCC","GM12878, Stanford","(-4.60395 bits) → 10.1053 bits","The information content of the binding site becomes positive, so a new NFKB binding site is created. ","EMSA demonstrated that the mutation creates a new binding site. ","Concordant","Schedel et al. An IgE-associated polymorphism in STAT6 alters NF- kB binding, STAT6 promoter activity, and mRNA expression. 2009"]
[null,null,null,null,"GGGACCGTCC → GGGACTGTCC","GM19099, Stanford","(-3.39511 bits) → 10.9444 bits","The information content of the binding site becomes positive, so a new NFKB binding site is created. ",null,"Concordant"]
[null,null,null,null,"GGGACCGTCC → GGGACTGTCC","GM19193, Stanford","5.98494 bits → 10.9169 bits","The information content of the binding site increases by 4.93196 bits, so NFKB binding increases by 24.93196 ≈ 30.53 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,null,null,null,"GGGACCGTCC → GGGACTGTCC","GM12891, Stanford","7.35957 bits → 10.5403 bits","The information content of the binding site increases by 3.18073 bits, so NFKB binding increases by 23.18073 ≈ 9.07 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,"rs2734648","NC_000003.12:g.46370349G>T","Human CCR5","GGTTGTTTCC → GGTTTTTTCC","GM12878, Stanford","10.0185 bits → 10.1395 bits","The information content of the binding site increases by 0.121 bit, so NFKB binding increases by 20.121 ≈ 1.08 folds.","EMSA showed that the T allele displayed greater binding than the G allele, and the G allele produced a weaker supershift complex.","Concordant","Bream et al. CCR5 Promoter Alleles and Specific DNA Binding Factors. 1999"]
[null,null,null,null,"GGTTGTTTCC → GGTTTTTTCC","GM19099, Stanford","9.35897 bits → 9.18321 bits","The information content of the binding site decreases by 0.17576 bit, so NFKB binding decreases by 20.17576 ≈ 1.13 folds.",null,"Discordant"]
[null,null,null,null,"GGTTGTTTCC → GGTTTTTTCC","GM19193, Stanford","8.88441 bits → 8.63996 bits","The information content of the binding site decreases by 0.24445 bit, so NFKB binding decreases by 20.24445 ≈ 1.18 folds.",null,"Discordant"]
[null,null,null,null,"GGTTGTTTCC → GGTTTTTTCC","GM12891, Stanford","9.39733 bits → 8.97852 bits","The information content of the binding site decreases by 0.41881 bit, so NFKB binding decreases by 20.41881 ≈ 1.34 folds.",null,"Discordant"]
[null,"rs3025058","NC_000011.10:g.102845217_102845218insA","Human MMP3","TGGTTTTTCC → GGTTTTTTCC","GM12878, Stanford","9.38525 bits → 10.1395 bits","The information content of the binding site increases by 0.75425 bit, so NFKB binding increases by 20.75425 ≈ 1.69 folds.","EMSA and competiton experiments showed that NFKB binds preferentially to the 6T allele. ","Concordant","Borghaei et al. NF-kappaB binds to a polymorphic repressor element in the MMP-3 promoter. 2004"]
[null,null,null,null,"TGGTTTTTCC → GGTTTTTTCC","GM19099, Stanford","9.59935 bits → 9.18321 bits","The information content of the binding site decreases by 0.41614 bit, so NFKB binding decreases by 20.41614 ≈ 1.33 folds.",null,"Discordant"]
[null,null,null,null,"TGGTTTTTCC → GGTTTTTTCC","GM19193, Stanford","9.57757 bits → 8.63996 bits","The information content of the binding site decreases by 0.93761 bit, so NFKB binding decreases by 20.93761 ≈ 1.92 folds.",null,"Discordant"]
[null,null,null,null,"TGGTTTTTCC → GGTTTTTTCC","GM12891, Stanford","9.3695 bits → 8.97852 bits","The information content of the binding site decreases by 0.39098 bit, so NFKB binding decreases by 20.39098 ≈ 1.31 folds.",null,"Discordant"]
[null,"N/A","NC_000007.14:g.81771616A>G","Human HGF","AGGAATTCTC → GGGAATTCTC","GM12878, Stanford","(-4.03387 bits) → 10.6058 bits","The information content of the binding site becomes positive, so a new NFKB binding site is created. ","The SNP assembles wild-type sequences into an NFKB binding site. However, The paper does not give specific experimental evidence. It only states that the conclusion was obtained by 'transcription factor binding analyses'. ","Concordant","Tian et al. Allelic mutations in noncoding genomic sequences construct novel transcription factor binding sites that promote gene overexpression. 2015"]
[null,null,null,null,"AGGAATTCTC → GGGAATTCTC","GM19099, Stanford","6.66804 bits → 10.2428 bits","The information content of the binding site increases by 3.57476 bits, so NFKB binding increases by 23.57476 ≈ 11.92 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,null,null,null,"AGGAATTCTC → GGGAATTCTC","GM19193, Stanford","7.57661 bits → 10.4857 bits","The information content of the binding site increases by 2.90909 bits, so NFKB binding increases by 22.90909 ≈ 7.51 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,null,null,null,"AGGAATTCTC → GGGAATTCTC","GM12891, Stanford","(-4.55923 bits) → 10.3247 bits","The information content of the binding site becomes positive, so a new NFKB binding site is created. ",null,"Concordant"]
[null,"rs3824934","NC_000011.10:g.101583757G>C","Human TRPC6","GGGGGTCTCC → CGGGGTCTCC","GM12878, Stanford","9.20535 bits → -5.43432 bits","The information content of the binding site becomes negative, so NFKB binding is abolished. ","EMSA and competiton experiments showed that NFKB binds specifically to the G allele. ","Concordant","Yu et al. A Functional Single-Nucleotide Polymorphism in the TRPC6 Gene Promoter Associated With Idiopathic Pulmonary Arterial Hypertension. 2009"]
[null,null,null,null,"GGGGGTCTCC → CGGGGTCTCC","GM19099, Stanford","10.3307 bits → 4.84682 bits","The information content of the binding site decreases by 5.48388 bits, so NFKB binding decreases by 25.48388 ≈ 44.75 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,null,null,null,"GGGGGTCTCC → CGGGGTCTCC","GM19193, Stanford","10.0177 bits → 5.76113 bits","The information content of the binding site decreases by 4.25657 bits, so NFKB binding decreases by 24.25657 ≈ 19.11 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,null,null,null,"GGGGGTCTCC → CGGGGTCTCC","GM12891, Stanford","10.5935 bits → -2.41603 bits","The information content of the binding site becomes negative, so NFKB binding is abolished. ",null,"Concordant"]
[null,"N/A","NC_000011.10:g.47395568G>A\nNC_000011.10:g.47395565G>A","Human SPI1","GGGCCTCCCC → GGGTCTTCCC","GM12878, Stanford","4.51781 bits → 11.0746 bits","The information content of the binding site increases by 6.55679 bits, so NFKB binding increases by 26.55679 ≈ 94.14 folds.","EMSA and competition experiments showed that the polymorphism increases the affinity of the binding site.","Concordant","Bonadies et al. PU.1 is regulated by NF-kB through a novel binding site in a 17 kb upstream enhancer element. 2010"]
[null,null,null,null,"GGGCCTCCCC → GGGTCTTCCC","GM19099, Stanford","6.97617 bits → 11.459 bits","The information content of the binding site increases by 4.48283 bits, so NFKB binding increases by 24.48283 ≈ 22.36 folds.",null,"Concordant"]
[null,null,null,null,"GGGCCTCCCC → GGGTCTTCCC","GM19193, Stanford","6.97548 bits → 11.3853 bits","The information content of the binding site increases by 4.40982 bits, so NFKB binding increases by 24.40982 ≈ 21.26 folds.",null,"Concordant"]
[null,null,null,null,"GGGCCTCCCC → GGGTCTTCCC","GM12891, Stanford","(-2.58968 bits) → 10.8488 bits","The information content of the binding site becomes positive, so a new NFKB binding site is created. ",null,"Qualitatively concordant, quantitatively discordant"]
[null,"rs6776243","NC_000003.12:g.69204505T>C","Human FRMD4B ","GGGGATCCCT → GGGGATCCCC\nAGGGATCCCC → GGGGATCCCC\nGAGGGATCCC → GGGGGATCCC","GM12878, Stanford","6.9127 bits → 8.26594 bits\n-6.37373 bits → 8.26594 bits\n-5.59709 bits → 8.97973 bits","The information content of the first binding site increases by 1.35324 bits, so NFKB binding increases by 21.35324 ≈ 2.55 folds. The information contents of the following two binding sites become positive, so new NFKB binding sites are created. ","EMSA-seq showed that the C allele has a higher NFKB binding potential.","Concordant","Wong et al. Extensive characterization of NF-kB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. 2011"]
[null,null,null,null,"GGGGATCCCT → GGGGATCCCC\nAGGGATCCCC → GGGGATCCCC","GM19099, Stanford","7.83393 bits → 9.84811 bits\n6.27334 bits → 9.84811 bits","The information content of the first binding site increases by 2.01418 bits, so NFKB binding increases by 22.01418 ≈ 4.04 folds. The information content of the second binding site increases by 3.57477 bits, so NFKB binding increases by 23.57477 ≈ 11.92 folds. ",null,"Concordant"]
[null,null,null,null,"GGGGATCCCT → GGGGATCCCC\nAGGGATCCCC → GGGGATCCCC\nGGGATCCCTC → GGGATCCCCC","GM19193, Stanford","7.23762 bits → 9.90502 bits\n6.99597 bits → 9.90502 bits\n0.429985 bit → 3.72778 bits","The information contents of the three binding sites increase by 2.6674, 2.90905, and 3.297785 bits, respectively. So NFKB binding increases by 6.35, 7.51, and 9.83 folds, respectively. ",null,"Concordant"]
[null,null,null,null,"GGGGATCCCT → GGGGATCCCC\nAGGGATCCCC → GGGGATCCCC\nGAGGGATCCC → GGGGGATCCC","GM12891, Stanford","7.82952 bits → 9.71836 bits\n-5.16557 bits → 9.71836 bits\n-5.0771 bits → 10.0812 bits","The information content of the first binding site increases by 1.88884 bits, so NFKB binding increases by 21.88884 ≈ 3.70 folds. The information contents of the following two binding sites become positive, so new NFKB binding sites are created. ",null,"Concordant"]
[null,"rs2430561","NC_000012.12:g.68158742T>A","Human IFNG","GTGTGATTTG → GTGAGATTTG","GM12878, Stanford","(-1.49232 bits) → 0.039578 bit","The information content of the binding site becomes positive, so a new NFKB binding site is created. ","EMSA showed specific NFKB binding to the mutant allele.","Concordant","Pravica et al. A single nucleotide polymorphism in the first intron of the human IFN-gamma gene: absolute correlation with a polymorphic CA microsatellite marker of high IFN-gamma production. 2000"]
[null,null,null,null,"No predicted binding site","GM19099, Stanford","N/A","N/A",null,"Discordant"]
[null,null,null,null,"No predicted binding site","GM19193, Stanford","N/A","N/A",null,"Discordant"]
[null,null,null,null,"No predicted binding site","GM12891, Stanford","N/A","N/A",null,"Discordant"]
["NFYA","rs34809449","NC_000011.10:g.5254895G>A","Human HBG2","GACCAATAGCCT → GACTAATAGCCT","K562, Stanford, SPP","8.13817 bits → -2.75827 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ","Gel retardation assays on various nuclear extracts demonstrated that this mutation abolishes NFY binding.","Concordant","Fucharoen et al. A novel C-T transition within the distal CCAAT motif of the G gamma-globin gene in the Japanese HPFH: implication of factor binding in elevated fetal globin expression. 1990"]
[null,null,null,null,"TGACCAATAGCC → TGACTAATAGCC","K562, Stanford, optimal IDR","9.03182 bits → -1.26734 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ",null,"Concordant"]
[null,"rs61663607","NC_000019.10:g.40851171T>C","Human CYP2A6","TCCCAATCAGAG → TCCCAGTCAGAG","K562, Stanford","9.37288 bits → 3.55338 bits","The information content of the binding site decreases by 5.8195 bits, so NFYA binding decreases by 25.8195 ≈ 56.47 folds.","EMSA demonstrated that the mutated C allele cannot compete efficiently with binding of the protein complex to the wild-type CCAAT box.","Concordant","Richter et al. Polymorphic NF-Y dependent regulation of human nicotine C-oxidase (CYP2A6). 2004"]
[null,null,null,null,"TTCCCAATCAGA → TTCCCAATCAGA","K562, Stanford, optimal IDR","8.97146 bits → 3.75969 bits","The information content of the binding site decreases by 5.21177 bits, so NFYA binding decreases by 25.21177 ≈ 37.06 folds.",null,"Concordant"]
[null,"rs281860601","NC_000011.10:g.5249971G>A","Human HBG1","GACCAATAGCCT → GACTAATAGCCT","K562, Stanford","8.13817 bits → -2.75827 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ","Gel retardation assays on various nuclear extracts demonstrated that this mutation abolishes NFY binding.","Concordant","Kutlar et al. THE GEORGIA TYPE OF NONDELETIONAL HEREDITARY PERSISTENCEOF FETAL HEMOGLOBIN HAS A C-T MUTATION AT NUCLEOTIDE -114 OF THE A Gamma-GLOBIN GENE. 1991"]
[null,null,null,null,"TGACCAATAGCC → TGACTAATAGCC","K562, Stanford, optimal IDR","9.03182 bits → -1.26734 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ",null,"Concordant"]
[null,"N/A","NC_000003.12:g.169765118G>C","Human TERC","GGCCAATCCGTG → GGGCAATCCGTG","K562, Stanford","9.85439 bits → 0.76652 bit","The information content of the binding site decreases by 9.08787 bits, so NFYA binding decreases by 29.08787 ≈ 544.15 folds.","The gel shift assay showed that the mutant allele did not bind to NFY.","Qualitatively concordant, quantitatively discordant","Aalbers et al. Human telomere disease due to disruption of the CCAAT box of the TERC promoter. 2012"]
[null,null,null,null,"TGGCCAATCCGT → TGGGCAATCCGT","K562, Stanford, optimal IDR","9.90371 bits → 0.913374 bit","The information content of the binding site decreases by 8.990336 bits, so NFYA binding decreases by 28.990336 ≈ 508.58 folds.",null,"Qualitatively concordant, quantitatively discordant"]
[null,"N/A","NC_000011.10:g.5227144A>T","Human beta-globin","GGCCAATCTACT → GGCCATTCTACT","K562, Stanford","6.08732 bits → -3.67704 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ","RTPCR analysis showed that after the mutation the mRNA level decreased to 19.35% of the normal level.","Concordant","Chen et al. A novel mutation of −73(A→ T) in the CCAAT box of the β-globin gene identified in a patient with the mild β-thalassemia intermedia. 2007"]
[null,null,null,null,"TGGCCAATCTAC → TGGCCATTCTAC","K562, Stanford, optimal IDR","6.60285 bits → -2.31597 bits","The information content of the binding site becomes negative, so NFYA binding is abolished. ",null,"Concordant"]
["NFYB","rs34809449","NC_000011.10:g.5254895G>A","Human HBG2","AGGCTATTGGTC → AGGCTATTAGTC","GM12878, HMS","9.04067 bits → -4.15968 bits","The information content of the binding site becomes negative, so NFYB binding is abolished. ","Gel retardation assays on various nuclear extracts demonstrated that this mutation abolishes NFY binding.","Concordant","Fucharoen et al. A novel C-T transition within the distal CCAAT motif of the G gamma-globin gene in the Japanese HPFH: implication of factor binding in elevated fetal globin expression. 1990"]
[null,"rs61663607","NC_000019.10:g.40851171T>C","Human CYP2A6","CTCTGATTGGGA → CTCTGACTGGGA","GM12878, HMS","9.81881 bits → 5.87885 bits","The information content of the binding site decreases by 3.93996 bits, so NFYB binding decreases by 23.93996 ≈ 15.35 folds.","EMSA demonstrated that the mutated C allele cannot compete efficiently with binding of the protein complex to the wild-type CCAAT box.","Concordant","Richter et al. Polymorphic NF-Y dependent regulation of human nicotine C-oxidase (CYP2A6). 2004"]
[null,"rs281860601","NC_000011.10:g.5249971G>A","Human HBG1","AGGCTATTGGTC → AGGCTATTAGTC","GM12878, HMS","9.04067 bits → -4.15968 bits","The information content of the binding site becomes negative, so NFYB binding is abolished. ","Gel retardation assays on various nuclear extracts demonstrated that this mutation abolishes NFY binding.","Concordant","Kutlar et al. THE GEORGIA TYPE OF NONDELETIONAL HEREDITARY PERSISTENCEOF FETAL HEMOGLOBIN HAS A C-T MUTATION AT NUCLEOTIDE -114 OF THE A Gamma-GLOBIN GENE. 1991"]
[null,"N/A","NC_000003.12:g.169765118G>C","Human TERC","CACGGATTGGCC → CACGGATTGCCC","GM12878, HMS","10.7434 bits → 2.52236 bits","The information content of the binding site decreases by 8.22104 bits, so NFYB binding decreases by 28.22104 ≈ 298.39 folds.","The gel shift assay showed that the mutant allele did not bind to NFY.","Qualitatively concordant, quantitatively discordant","Aalbers et al. Human telomere disease due to disruption of the CCAAT box of the TERC promoter. 2012"]
[null,"N/A","NC_000011.10:g.5227144A>T","Human beta-globin","AGTAGATTGGCC → AGTAGAATGGCC","GM12878, HMS","7.54937 bits → -1.71879 bits","The information content of the binding site becomes negative, so NFYB binding is abolished. ","RTPCR analysis showed that after the mutation the mRNA level decreased to 19.35% of the normal level.","Concordant","Chen et al. A novel mutation of −73(A→ T) in the CCAAT box of the β-globin gene identified in a patient with the mild β-thalassemia intermedia. 2007"]
["PU1","rs11568070 ","NC_000017.11:g.4641943G>A","Human ALOX15","TGATTCCCTCTTCCTG → TGATTTCCTCTTCCTG","HC-60, HAIB, Rep1","(-3.54072 bits) → 13.8532 bits","The information content of the binding site becomes positive, so a new PU1 binding site is created. ","EMSA demonstrated that PU1 can only bind to the A allele.","Concordant","Wittwer et al. Functional Polymorp hism in ALOX15 Results in Increased Allele-Specific Transcription in Macrophages Through Binding of the Transcription Factor SPI1. 2006"]
[null,null,null,null,"GGAAGAGGGAATCAAC → GGAAGAGGAAATCAAC","GM12891, HAIB","(-0.62289 bit) → 12.5186 bits","The information content of the binding site becomes positive, so a new PU1 binding site is created. ",null,"Concordant"]
["SP1","rs6918698","NC_000006.12:g.131952117G>C","Human CTGF","GGGAGGAGTGGC → GGGACGAGTGGC","GM12878, HAIB","7.73218 bits → -3.14373 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","EMSA demonstrated that the mutation eliminates SP1 binding.","Concordant","Fonseca et al. A Polymorphism in the CTGF Promoter Region Associated with Systemic Sclerosis. 2007"]
[null,"rs1800590","NC_000008.11:g.19939160T>G","Human LPL","GGGGGGAGGGAC → GGGGGGAGGGCC","GM12878, HAIB","13.5488 bits → 10.1767 bits","The information content of the binding site decreases by 3.3721 bits, so SP1 binding decreases by 23.3721 ≈ 10.35 folds.","EMSA, competition and supershift experiments demonstrated that the G allele exhibits a lower affinity for Sp1 than the wild-type T allele.","Concordant","Yang et al. Sp1 and Sp3 transactivate the human lipoprotein lipase gene promoter through binding to a CT element: synergy with the sterol regulatory element binding protein and reduced transactivation of a naturally occurring promoter variant. 1998"]
[null,"rs17860508","NC_000005.10:g.159333192_159333197delTTAGAGinsGC","Human IL-12B","CTAATGTGGGGG (included in the EMSA probe, but does not contain the SNP)\n → \nAGAGGGCTGTGG","GM12878, HAIB","2.16903 bits → 9.44436 bits","The information content of the binding site increases by 7.27533 bits, so SP1 binding to the probe increases by 27.27533 ≈ 154.91 folds.","EMSA, competition experiments and supershift experiments demonstrated that the GC allele exhibits a higher affinity for Sp1 than the TTAGAG allele.","Concordant","Shimokawa et al. Functional analysis of a polymorphism in the promoter region of the IL-12/23p40 gene. 2008"]
[null,"rs765424821","NC_000005.10:g.132257678_132257689delCGGCGGCGGCTC","Human RIL","CTGAGGAGGAGC → No binding site in the probe","GM12878, HAIB","9.21444 bits → N/A","The allele containing the inserted fragment is a binding site, whereas the other allele is not.","EMSA demonstrated that the insertion created a new SP1/SP3 binding site.","Concordant","Boumber et al. An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection. 2008"]
[null,"rs28095","NC_000005.10:g.52989287T>C","Human ITGA2","GAGGGGCGGGCT → GAGGGGCGGGCC\nGCGGGCTGGGGC → GCGGGCCGGGGC","GM12878, HAIB","6.80364 bits → 9.50467 bits\n4.8675 bits → 6.92812 bits","The information contents of the binding sites increase by 2.70103 or 2.06062 bits, so SP1 binding increases by 22.70103 or 22.06062 ≈ 6.5027 or 4.1717 folds.","In mobility shift analyses, the T substitution attenuates complex formation with both Sp1 and Sp3. ","Concordant","Jacquelin et al. Allele-dependent transcriptional regulation of the human integrin α2 gene. 2001"]
[null,"rs73717525","NC_000007.14:g.117479869G>T","Human CFTR","TGGGGCCGGACC → TGGGGCCTGACC","GM12878, HAIB","2.25459 bits → 0.238698 bit","The information content of the binding site decreases by 2.015892 bits, so SP1 binding decreases by 22.015892 ≈ 4.04 folds.","EMSA demonstrated that the mutation decreases the strength of the SP1 binding site.","Concordant","Taulan et al. First functional polymorphism in CFTR promoter that results in decreased transcriptional activity and Sp1/USF binding. 2007"]
[null,"rs2020918","NC_000008.11:g.42214920A>G","Human PLAT","CTGGGGCAGGCT → CTGGGGCGGGCT","GM12878, HAIB","2.84969 bits → 4.16372 bits","The information content of the binding site increases by 1.31403 bits, so SP1 binding increases by 21.31403 ≈ 2.49 folds.","EMSA, supershift and cross-competition experiments indicated an greater protein binding affinity to the G allele as compared with the A allele variant.","Concordant","Wolf et al. The t-PA 7351C>T enhancer polymorphism decreases Sp1 and Sp3 protein binding affinity and transcriptional responsiveness to retinoic acid. 2004"]
[null,"rs2077079","NC_000002.12:g.85668215T>G","Human SFTPB","ACCAAGCAGGGT → TTGGGGCATGGC (two strands)","GM12878, HAIB","1.04957 bits → 4.42861 bits","The information content of the binding site increases by 3.37904 bits, so SP1 binding increases by 23.37904 ≈ 10.40 folds.","EMSA demonstrated that the T allele is a weaker binding site than the G allele.","Concordant","Steagall et al. The C/A (-18) polymorphism in the surfactant protein B gene influences transcription and protein levels of surfactant protein B. 2007"]
[null,"rs117039649","NC_000012.12:g.68808776G>C","Human MDM2","GGGGGCCGGGGG → GCGGGCCGGGGG","GM12878, HAIB","9.46875 bits → 6.43989 bits","The information content of the binding site decreases by 3.02886 bits, so SP1 binding decreases by 23.02886 ≈ 8.16 folds.","BIA demonstrated that SNP285G>C diminishes Sp1 transcription factor\nbinding to the MDM2 Promoter.","Concordant","Knappskog et al. The MDM2 Promoter SNP285C/309G Haplotype Diminishes Sp1 Transcription Factor Binding and Reduces Risk for Breast and Ovarian Cancer in Caucasians. 2011"]
[null,"rs1862513","NC_000019.10:g.7668907C>G","Human RETN","ATGAAGACGGAG → ATGAAGAGGGAG","GM12878, HAIB","(-8.88151 bits) → 5.96275 bits","The information content of the binding site becomes positive, so a new SP1 binding site is created. ","EMSA demonstrated that SP1 specifically binds to the G allele.","Concordant","Chung et al. Regulation of human resistin gene expression in cell systems: an important role of stimulatory protein 1 interaction with a common promoter polymorphic site. 2005\nOsawa et al. The G/G genotype of a resistin single-nucleotide polymorphism at -420 increases type 2 diabetes mellitus susceptibility by inducing promoter activity through specific binding of Sp1/3. 2004"]
[null,"rs890293","NC_000001.11:g.59926822C>A","Human CYP2J2","GCGAGGCGGGGC → GCTAGGCGGGGC","GM12878, HAIB","12.2238 bits → 9.75035 bits","The information content of the binding site decreases by 2.47345 bits, so SP1 binding decreases by 22.47345 ≈ 5.55 folds.","EMSA demonstrated that the A allele significantly reduced SP1 binding.","Concordant","Spiecker et al. Risk of coronary artery disease associated with polymorphism of the cytochrome P450 epoxygenase CYP2J2. 2004"]
[null,"rs28357094","NC_000004.12:g.87975645T>G","Human OPN","GGGAGGCGGAGA → GGGAGGCGGCGA","GM12878, HAIB","13.2346 bits → 5.68302 bits","The information content of the binding site decreases by 7.55158 bits, so SP1 binding decreases by 27.55158 ≈ 187.61 folds.","Differences in intensity were appreciable for the two alternative probes and cross-competitions highlighted that the oligonucleotide with the T allele contained a higher affinity binding site than the G allele.","Concordant","Giacopelli et al. Polymorphisms in the osteopontin promoter affect its transcriptional activity. 2004"]
[null,"rs3760687","NC_000019.10:g.7702508C>T","Human FCER2","TCATGGTGGGGT → TCATGGTGGAGT","GM12878, HAIB","1.82007 bits → 0.416417 bit","The information content of the binding site decreases by 1.403653 bits, so SP1 binding decreases by 21.403653 ≈ 2.65 folds.","EMSA demonstrated that SP1 preferentially binds to the C allele.","Concordant","Potaczek et al. Interaction of functional FCER2 promoter polymorphism and phenotype-associated haplotypes. 2009"]
[null,"rs181096360","NC_000002.12:g.47783024C>T","Human MSH6","GAAGGGCGGGGC → GAAGGACGGGGC","GM12878, HAIB","13.1574 bits → -2.39108 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","EMSA showed that the mutation eliminates the binding site.","Concordant","Gazzoli et al. Regulation of the Human MSH6 Gene by the Sp1 Transcription Factor and Alteration of Promoter Activity and Expression by Polymorphisms. 2003"]
[null,"rs3957356 ","NC_000006.12:g.52803872T>C","Human GSTA1","AGTGGGAGAGAA → AGTGGGAGGGAA","GM12878, HAIB","(-5.22525 bits) → 10.3286 bits","The information content of the binding site becomes positive, so a new SP1 binding site is created. ","EMSA showed that the T allele is not a binding site.","Concordant","Morel et al. The human glutathione transferase alpha locus: genomic organization of the gene cluster and functional characterization of the genetic polymorphism in the hGSTA1 promoter. 2002"]
[null,"rs11568816","NC_000004.12:g.99088772G>A","Human ADH3","CATGGGCGTGGC → CATGGGCGTAGC","GM12878, HAIB","4.50287 bits → 3.09922 bits","The information content of the binding site decreases by 1.40365 bits, so SP1 binding decreases by 21.40365 ≈ 2.65 folds.","EMSA showed that the G allele is a stronger binding site than the A allele for SP1.","Concordant","Hedberg et al. Functional polymorphism in the alcohol dehydrogenase 3 (ADH3) promoter. 2001"]
[null,"rs540289812","NC_000003.12:g.169765159G>C","Human TERC","CTCGGGCGGGCT → CTCCGGCGGGCT","GM12878, HAIB","0.212966 bit → -11.553624 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","EMSA showed that the mutation abolished SP1 binding. Supershift analysis demonstrated that the wild-type G allele is a low-affinity binding site in vitro.","Concordant","Keith et al. A mutation in a functional Sp1 binding site of the telomerase RNA gene (hTERC) promoter in a patient with Paroxysmal Nocturnal Haemoglobinuria. 2004"]
[null,"rs8179090","NC_000017.11:g.78925807C>G","Human TIMP2","CCGAGGCTGGGC → CCGACGCTGGGC","GM12878, HAIB","9.08316 bits → -1.79275 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","The binding site is abolished by the substituion.","Concordant","Hirano et al. Tissue inhibitor of metalloproteinases-2 gene polymorphisms in chronic obstructive pulmonary disease. 2000\nO-charoenrat et al. The role of genetic polymorphisms in the promoters of the matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-2 genes in head and neck cancer. 2006"]
[null,"rs1800012","NC_000017.11:g.50200388C>A","Human COLIA1","TGGGGGCGGGAT → TGTGGGCGGGAT","GM12878, HAIB","10.6659 bits → 8.19247 bits","The information content of the binding site decreases by 2.47343 bits, so SP1 binding decreases by 22.47343 ≈ 5.55 folds.","Preliminary studies have shown the affinity of Sp1 to the wild-type allele is higher than to the mutant allele in COLIA1.","Concordant","Grant et al. Reduced bone density and osteoporosis associated with a polymorphic Sp1 binding site in the collagen type I alpha 1 gene. 1996\nLANGDAHL et al. An Sp1 Binding Site Polymorphism in the COLIA1 Gene Predicts Osteoporotic Fractures in Both Men and Women. 1998\nMeyer et al. Association of COLIA1 Sp1 polymorphism with the effect of subcutaneously injected recombinant hGH in GH-deficient adults. 2008"]
[null,"rs41261045","NC_000022.11:g.25564658G>A","Human GRK3","GAGGGGAGGGCG → GAGGAGAGGGCG","GM12878, HAIB","8.35513 bits  → 5.27915 bits","The information content of the binding site decreases by 3.07598 bits, so SP1 binding decreases by 23.07598 ≈ 8.43 folds.","In EMSA SP1 binding to the A allele is not detectable.","Qualitatively concordant, quantitatively discordant","Zhou et al. Promoter Variant in the GRK3 Gene Associated with Bipolar Disorder Alters Gene Expression. 2008"]
[null,"rs9943582","NC_000011.10:g.57237593T>C","Human AGTRL1","GGATGGAAGGGG → GATGGGAGGGGG","GM12878, HAIB","7.99021 bits  → 11.3372 bits","The information content of the binding site increases by 3.34699 bits, so SP1 binding increases by 23.34699 ≈ 10.58 folds.","The authors found the specific binding of SP1 to the G allele, but not the A allele.","Qualitatively concordant, quantitatively discordant","Hata et al. Functional SNP in an Sp1-binding site of AGTRL1 gene is associated with susceptibility to brain infarction. 2007"]
[null,"N/A","NC_000019.10:g.11089411T>C","Human LDLR ","AGGGGGAGGAGT → AGGGGGGGGAGT","GM12878, HAIB","11.3951 bits  → 0.565007 bit","The information content of the binding site decreases by 10.830093 bits, so SP1 binding decreases by 210.830093 ≈ 1820.47 folds.","Competition experiments showed that the affinity of the mutant\noligonucleotide for Spl was lower than that of the normal oligonucleotide.","Concordant","Sun et al. A mutation (T-45C) in the promoter region of the lowdensity-lipoprotein (LDL)-receptor gene is associated with a mild clinical phenotype in a patient with heterozygous familial hypercholesterolaemia (FH). 1995"]
[null,"N/A","NC_001802.1:g.9012C>T","HIV1 genome","GGGAGGCGTGGC → GGGAGGTGTGGC","GM12878, HAIB","8.39348 bits → 6.33285 bits","The information content of the binding site decreases by 2.06063 bits, so SP1 binding decreases by 22.06063 ≈ 4.17 folds.","EMSA showed that the T allele is a lower-affinity binding site.","Concordant","Shah et al. Functional properties of the HIV-1 long terminal repeat containing single-nucleotide polymorphisms in Sp site III and CCAAT/enhancer binding protein site I. 2014"]
[null,"N/A (artificial)","NC_000012.12:g.53380115G>C","Human SP1","ATTGGGCGGGGC → ATTGGGCCGGGC","GM12878, HAIB","10.8391 bits → -4.00516 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","EMSA demonstrated that the mutation abolished SP1 binding.","Concordant","Nicolas et al. Transcriptional regulation of the human Sp1 gene promoter by the specificity protein (Sp) family members nuclear factor Y (NF-Y) and E2F. 2003"]
[null,"rs55924981","NC_000015.10:g.39588473G>A","Human TSP1","CAAGGGAGGGAT → CAAGAGAGGGAT","GM12878, HAIB","6.58692 bits → 3.51094 bits","The information content of the binding site decreases by 3.07598 bits, so SP1 binding decreases by 23.07598 ≈ 8.43 folds.","EMSA demonstrated that the mutation decreased and/or eliminated\nlocal binding of SP1, and the mutant oligo bound SP1 poorly.","Concordant","Maloney et al. Loss-of-function thrombospondin-1 mutations in familial pulmonary hypertension. 2011"]
[null,"rs3815578\nrs3815577\nrs3815579\nrs3815580\n rs3815581\nrs373304082\nrs113176016                 ","NC_000016.10:g.55760553G>T\nNC_000016.10:g.55760552G>C\nNC_000016.10:g.55760558C>G\nNC_000016.10:g.55760559A>G\nNC_000016.10:g.55760562G>C    NC_000016.10:g.55760563_55760564insG\nNC_000016.10:g.55760567G>T","Human CES1A2","These SNPs change two binding sites from GGGGGCCAGGGT & GGTAACTGGGGG\nto\nTCTGGGCGGGGC & GCGGGGCTGGGC.","GM12878, HAIB","5.94193 bits & 0.817807 bits\n→ \n9.94804 bits & 11.2488 bits","The information contents of the binding sites increases, so SP1 binding increases.","EMSA demonstrated that the haplotype 'GTGCAGGGCGGTAACTctGGGCggGGcTGGgCtCC' possesses a stronger SP1 binding activity than 'GTGCAGGGCGGTAACTggGGGCcaGGgTGGCgCC'.\n.","Concordant","Yoshimura et al. Functional polymorphisms in carboxylesterase1A2 (CES1A2) gene involves specific protein 1 (Sp1) binding sites. 2008"]
[null,"rs2236141","NC_000022.11:g.28741882C>T","Human CHEK2","GGCGGCAGGGGA → AGCGGCAGGGGA","GM12878, HAIB","4.73053 bits → 4.59809 bits","The information content of the binding site decreases by 0.13244 bits, so SP1 binding decreases by 20.13244 ≈ 1.10 folds.","EMSA revealed that both of the two allleles are SP1 binding sites. When they are unmethylated there is no marked difference between their strengths, but when methylated the wild-type allele displays higher binding affinity. ","Concordant","Zhang et al. A variant in the CHEK2 promoter at a methylation site relieves transcriptional repression and confers reduced risk of lung cancer. 2010"]
[null,"rs5746092","NC_000006.12:g.159693279G>C","Human SOD2","GGGGAGCAGGGC → CGGGAGCAGGGC","GM12878, HAIB","11.9035 bits → 10.7788 bits","The information content of the binding site decreases by 1.1247 bits, so SP1 binding decreases by 21.1247 ≈ 2.18 folds.","EMSA showed that the mutation creates an SP1 binding site.","Discordant","Xu et al. Mutations in the SOD2 Promoter Reveal a Molecular Basis for an AP-2-Dependent Dysregulation of MnSOD Expression in Cancer Cells. 2008"]
[null,"N/A","NC_000013.11:g.113105748C>G ","Human F7","TGGGGGAGGGGA → TGGCGGAGGGGA","GM12878, HAIB","14.1746 bits  → 2.40806 bits","The information content of the binding site decreases by 11.76654 bits, so SP1 binding decreases by 211.76654 ≈ 3481.61 folds.","EMSA demonstrated that purified SP1 binding to the mutant allele is not detectable.","Qualitatively concordant, quantitatively discordant","Carew et al. Severe Factor VII Deficiency Due to a Mutation Disrupting an Sp1 Binding Site in the Factor VII Promoter. 1998"]
[null,"rs35617911","NC_000011.10:g.5254983G>C","Human HBG2","GTGGGGAAGGGG → GTGGGGAAGGCG","GM12878, HAIB","10.9814 bits → 5.5259 bits","The information content of the binding site decreases by 5.4555 bits, so SP1 binding decreases by 25.4555 ≈ 43.88 folds.","Mobility shift binding assays showed that the normal allele has a dramatically lower affiniy than the mutant allele.","Discordant","SYKES et al. A Naturally Occurring Gamma Globin Gene Mutation Enhances SP1 Binding Activity. 1990"]
[null,"rs41540312","NC_000002.12:g.47783075C>T","Human MSH6","CGCGGGCGGTGC → CGCAGGCGGTGC","GM12878, HAIB","8.80827 bits → 7.76738 bits","The information content of the binding site decreases by 1.04089 bits, so SP1 binding decreases by 21.04089 ≈ 2.06 folds.","EMSA showed that the mutation eliminates the binding site, because the SNP completely eliminated the ability of the oligonucleotide\nto act as a competitor of complex formation.","Qualitatively concordant, quantitatively discordant","Gazzoli et al. Regulation of the Human MSH6 Gene by the Sp1 Transcription Factor and Alteration of Promoter Activity and Expression by Polymorphisms. 2003"]
[null,"rs243865","NC_000016.10:g.55477894C>T","Human MMP2","AAGAGGTGGAGT → AAGAGGTAGAGT","GM12878, HAIB","7.62157 bits → 6.30755 bits","The information content of the binding site decreases by 1.31402 bits, so SP1 binding decreases by 21.31402 ≈ 2.49 folds.","Electrophoretic mobility shift assays demonstrated that Sp1 can bind to the C allele but not the T allele.","Qualitatively concordant, quantitatively discordant","Price et al. Identification of Novel, Functional Genetic Variants in the Human Matrix Metalloproteinase-2 Gene. 2001"]
[null,"rs2870820","NC_000012.12:g.68808546C>T","Human MDM2","CGATAGAGGGGA → CGATAGAAGGGA","GM12878, HAIB","4.97737 bits → 3.66334 bits","The information content of the binding site decreases by 1.31403 bits, so SP1 binding decreases by 21.31403 ≈ 2.49 folds.","BIA demonstrated that transcription factor Sp1 bound, insignificantly, but more easily to SNP55T than SNP55C.","Discordant","Okamoto et al. SNP55, a new functional polymorphism of MDM2-P2 promoter, contributes to allele-specific expression of MDM2 in endometrial cancers. 2015"]
[null,"rs41318021","NC_000013.11:g.29514470G>A","Human SLC7A1","GGGGGGCGGGGC → GGGGGGCGAGGC","GM12878, HAIB","16.2935 bits → 0.739692 bit","The information content of the binding site decreases by 15.553808 bits, so SP1 binding decreases by 215.553808 ≈ 48101.96 folds.","EMSA demonstrated that the only the allele G, but not the allele A, probe could bind to recombinant human SP1 protein.","Qualitatively concordant, quantitatively discordant","Yang et al. Mechanistic Insights Into the Link Between a Polymorphism of the 3'UTR of the SLC7A1 Gene and Hypertension. 2008"]
[null,"rs4376531","NC_000008.11:g.1906652C>G","Human ARHGEF10","AGGTGGATGTGC → AGGTGGATCTGC","GM12878, HAIB","7.03716 bits → -8.51669 bits","The information content of the binding site becomes negative, so SP1 binding is abolished. ","EMSA showed that the mutant allele is a stronger site than the normal allele for SP1.","Discordant","Matsushita et al. Functional SNP of ARHGEF10 confers risk of atherothrombotic stroke. 2010"]
[null," rs140941229\n& \nrs149785805","NC_000009.12:g.78032143G>A\n&\nNC_000009.12:g.78032144C>A","Human GNAQ","CCCGGGCTGGGC → CCCGGGCTGGAA","GM12878, HAIB","6.1733 bits → 3.4755 bits","The information content of the binding site decreases by 2.6978 bits, so SP1 binding decreases by 22.6978 ≈ 6.49 folds.","EMSA demonstrated that the TT allele eliminates SP1 binding.","Qualitatively concordant, quantitatively discordant","Liggett et al. A functional polymorphism of the Gαq (GNAQ) gene is associated with accelerated mortality in African-American heart failure. 2007"]
[null," rs712829","NC_000007.14:g.55019062G>T","Human EGFR","GGGGGGCGGAGG → GGGGGGAGGAGG","GM12878, HAIB","14.4017 bits → 13.7404 bits","The information content of the binding site decreases by 0.6613 bit, so SP1 binding decreases by 20.6613 ≈ 1.58 folds.","EMSA showed that the affinity of pure human Sp1 proteins to the T allele was significantly higher than that to the G allele.","Discordant","Liu et al. A Functional Common Polymorphism in a Sp1 Recognition Site of the Epidermal Growth Factor Receptor Gene Promoter. 2005"]
["SRF","rs35118767","NC_000005.10:g.148824138A>G","Human ADRB2","CCAATTTTGG → CCAGTTTTGG, +\nCCAAAATTGG → CCAAAACTGG, -","HepG2, HAIB","5.74254 bits → 4.07544 bits\n10.3971 bits → 11.0934 bits","The information content of the binding site on the positive strand decreases by 1.6671 bits, so SRF binding decreases by 21.6671 = 3.18 folds. The information content of the binding site on the negative strand increases by 0.6963 bit, so SRF binding increases by 20.6963 = 1.62 folds. Thus if the recognition of the two sites by SRF is equally likely, the overall effect of the SNP is to reduce SRF binding.","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCAATTTTGG → CCAGTTTTGG, +\nCCAAAATTGG → CCAAAACTGG, -","H1-hESC, HAIB","2.13329 bits → 0.988359 bit\n8.01922 bits → 9.16091 bits","The information content of the binding site on the positive strand decreases by 1.144931 bits, so SRF binding decreases by 21.144931 = 2.211 folds. The information content of the binding site on the negative strand increases by 1.14169 bits, so SRF binding increases by 21.14169 = 2.206 folds. Thus provided that the recognition of the two sites by SRF is equally likely, the overall effect of the SNP is to reduce SRF binding.",null,"Concordant"]
[null,"rs61805969","NC_000001.11:g.110677447C>T","Human KCNA3","CCAAAAATGG → TCAAAAATGG, +\nCCATTTTTGG → CCAAAACTGA, -","HepG2, HAIB","13.6516 bits → 9.86323 bits\n5.39496 bits → -0.67486 bit","The information content of the binding site on the positive strand decreases by 3.78837 bits, so SRF binding decreases by 23.78837 = 13.82 folds. The information content of the binding site on the negative strand becomes negative, so SRF binding is abolished.","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCAAAAATGG → TCAAAAATGG, +\nCCATTTTTGG → CCAAAACTGA, -","H1-hESC, HAIB","12.7052 bits → 7.15528 bits\n2.10729 bits → -11.61876 bits","The information content of the binding site on the positive strand decreases by 5.54992 bits, so SRF binding decreases by 25.54992 = 46.85 folds. The information content of the binding site on the negative strand becomes negative, so SRF binding is abolished.",null,"Concordant"]
[null,"rs62530172","NC_000008.11:g.84707992G>T","Human RALYL","CCAATTAAGG → CCAATTAAGT, +\nCCTTAATTGG → ACTTAATTGG, -","HepG2, HAIB","9.82333 bits → -3.91659 bits\n8.24286 bits → 4.5226 bits","The information content of the binding site on the positive strand becomes negative, so SRF binding is abolished. The information content of the binding site on the negative strand decreases by 3.72026 bits, so SRF binding decreases by 23.72026 = 13.18 folds.","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCAATTAAGG → CCAATTAAGT, +\nCCTTAATTGG → ACTTAATTGG, -","H1-hESC, HAIB","8.12534 bits → -5.60071 bits\n6.46105 bits → 0.941361 bit","The information content of the binding site on the positive strand becomes negative, so SRF binding is abolished. The information content of the binding site on the negative strand decreases by 5.519689 bits, so SRF binding decreases by 25.519689 = 45.88 folds.",null,"Concordant"]
[null,"rs10795076","NC_000010.11:g.3783151G>T","Human KLF6","CCAAATAAGG → CCAAATAAGT, +\nCCTTATTTGG → ACTTATTTGG, -","HepG2, HAIB","14.8338 bits → 1.09387 bits\n8.59875 bits → 4.87849 bits","The information content of the binding site on the positive strand decreases by 13.73993 bits, so SRF binding decreases by 213.73993 = 13681.42 folds. The information content of the binding site on the negative strand decreases by 3.72026 bits, so SRF binding decreases by 23.72026 = 13.18 folds.","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCAAATAAGG → CCAAATAAGT, +\nCCTTATTTGG → ACTTATTTGG, -","H1-hESC, HAIB","15.176 bits → 1.44995 bits\n7.62579 bits → 2.10609 bits","The information content of the binding site on the positive strand decreases by 13.72605 bits, so SRF binding decreases by 213.72605 = 13550.42 folds. The information content of the binding site on the negative strand decreases by 5.5197 bits, so SRF binding decreases by 25.5197 = 45.88 folds.",null,"Concordant"]
[null,"rs3763079","NC_000005.10:g.177426410T>C","Human GRK6","CCCTAATTGG → CCCTAACTGG, +\nCCAATTAGGG → CCAGTTAGGG, -\nGCCAATTAGG → GCCAGTTAGG, -","HepG2, HAIB","8.38498 bits → 9.0813 bits\n1.32619 bits → -0.340912 bit\n6.43116 bits → 3.85643 bits","The information content of the first binding site increases by 0.69632 bit, so SRF binding decreases by 20.69632  = 1.62 folds. The information content of the second binding site becomes negative, so SRF binding is abolished. The information content of the third binding site decreases by 2.57473 bits, so SRF binding decreases by 22.57473  = 5.96 folds. Thus the overall effect of this SNP is to reduce SRF binding. ","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCCTAATTGG → CCCTAACTGG, +\nGCCAATTAGG → GCCAGTTAGG, -","H1-hESC, HAIB","6.41845 bits → 7.56014 bits\n5.68262 bits → 3.56501 bits","The information content of the first binding site increases by 1.14169 bits, so SRF binding decreases by 21.14169  = 2.21 folds. The information content of the second binding site decreases by 2.11761 bits, so SRF binding decreases by 22.11761  = 4.34 folds. Thus the overall effect of this SNP is to reduce SRF binding. ",null,"Concordant"]
[null,"rs13037347","NC_000020.11:g.32207323T>C","Human PLAGL2","CCTTATCTGG → CCTTACCTGG, +\nCCAGATAAGG → CCAGGTAAGG, -","HepG2, HAIB","9.29507 bits → 6.8408 bits\n13.1667 bits → 10.5919 bits","The information content of the binding site on the positive strand decreases by 2.45427 bits, so SRF binding decreases by 22.45427 = 5.48 folds. The information content of the binding site on the negative strand decreases by 2.5748 bits, so SRF binding decreases by 22.5748 = 5.96 folds.","EMSA demonstrated that the mutation attenuates SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCTTATCTGG → CCTTACCTGG, +\nCCAGATAAGG → CCAGGTAAGG, -","H1-hESC, HAIB","8.76748 bits → 5.3126 bits\n14.0311 bits → 11.9135 bits","The information content of the binding site on the positive strand decreases by 2.45427 bits, so SRF binding decreases by 22.45427 = 5.48 folds. The information content of the binding site on the negative strand decreases by 2.5748 bits, so SRF binding decreases by 22.5748 = 5.96 folds.",null,"Concordant"]
[null,"rs16958232","NC_000016.10:g.68647480A>G","Human CDH3","CCTTTAGAGG → CCTTTAGGGG, +\nCCTCTAAAGG → CCCCTAAAGG, -","HepG2, HAIB","4.14251 bits → -4.35463 bits\n5.12013 bits → 5.26225 bits ","The information content of the binding site on the positive strand becomes negative, so SRF binding is abolished. The information content of the binding site on the negative strand increases by 0.14212 bit, so SRF binding increases by 20.14212 = 1.10 folds. Thus the overall effect of this SNP is to enhance SRF binding. ","EMSA demonstrated that the mutation enhances SRF binding.","Concordant","Benson et al. Identifying functional single nucleotide polymorphisms in the human CArGome. 2011"]
[null,null,null,null,"CCTTTAGAGG → CCTTTAGGGG, +\nCCTCTAAAGG → CCCCTAAAGG, -","H1-hESC, HAIB","3.12423 bits → -8.1822 bits\n1.91411 bits → 1.87152 bits","The information content of the binding site on the positive strand becomes negative, so SRF binding is abolished. The information content of the binding site on the negative strand decreases by 0.04259 bit, so SRF binding decreases by 20.14212 = 1.03 folds. Thus the overall effect of this SNP is to reduce SRF binding. ",null,"Discordant"]
["STAT1","rs1800682","NC_000010.11:g.88990206A>G","Human FAS","TTCCAGAA → TTCCAGGAA\nTTCTGGAA → TTCCTGGAA","HeLa-S3, Yale\nTreated with IFNg for 30 minutes","11.1088 bits → 11.2374 bits\n11.1088 bits → 11.2374 bits","The information content of the binding site increases by 0.1286 bit, so STAT1 binding increases by 20.1286 ≈ 1.09 folds.","EMSA experiment was repeated several times with no detectable difference in band intensity between the A allele and the G allele, both variants can bind STAT1 equally well.","Concordant","Sibley et al. Functional FAS Promoter Polymorphisms Are Associated with Increased Risk of Acute Myeloid Leukemia. 2003"]
["USF1","rs2853542","NC_000018.10:g.657685G>C","Human TS","GGCCAAGTGG → GGCGAAGTGG\nCGCCACTTGG → CGCCACTTCG","H1-hESC, HAIB","1.7359 bits → -14.34224 bits\n1.30714 bits → -9.15086 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","EMSA showed that the mutation abolished USF1 binding.","Concordant","Mandola et al. A Novel Single Nucleotide Polymorphism within the 5 Tandem Repeat Polymorphism of the Thymidylate Synthase Gene Abolishes USF-1 Binding and Alters Transcriptional Activity. 2003"]
[null,"rs1135534 ","NC_000004.12:g.54228348C>A","Human PDGFRA","ACCCACGCGG → ACCCAAGCGG","H1-hESC, HAIB","1.87143 bits → -9.01 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","EMSA demonstrated that the A allele is not a binding site.","Concordant","Toepoel et al. Haplotype-dependent binding of nuclear proteins to the promoter of the neural tube defects-associated platelet-derived growth factor alpha-receptor gene. 2005"]
[null,"rs2071592","NC_000006.11:g.31515340T>A","Human IKBL","ACGCAGGTGG → ACGCTGGTGG","H1-hESC, HAIB","3.92674 bits → -5.84949 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","Supershift studies confirmed that USF1 binds to the T allele, but not the mutated A allele.","Concordant","Boodhoo et al. A promoter polymorphism in the central MHC gene, IKBL, influences the binding of transcription factors USF1 and E47 on disease-associated haplotypes. 2004"]
[null,"rs661204","NC_000011.10:g.69516215G>A","Human CCND1","GATCATGGGG → GATTATGGGG\nCACCCCATGA → CACCCCATAA","H1-hESC, HAIB","1.57185 bits → -14.50629 bits\n1.40593 bits → -12.00385 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","EMSA showed that the A allele is not a binding site.","Concordant","French et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. 2013"]
[null,"rs5050","NC_000001.11:g.230714140T>G","Human AGT","GGTCACGATG → GGTCACGAGG\nGGCATCGTGA → GGCCTCGTGA","H1-hESC, HAIB","1.15439 bits → 9.48339 bits\n-10.5342 bits → 2.88104 bits","The information content of the binding site increases by 8.329 bits, so USF1 binding increases by 28.329 ≈ 321.57 folds.","EMSA showed that the G allele is a stronger binding site than the T allele for USF.","Concordant","Zhao et al. Role of C/A Polymorphism at -20 on the Expression of Human Angiotensinogen Gene. 1999\nDickson et al. Upstream stimulatory factor is required for human angiotensinogen expression and differential regulation by the A-20C polymorphism. 2008"]
[null,"rs3093062","NC_000001.11:g.159714894C>T","Human CRP","TACCACGTGC → TACCACGTAC","H1-hESC, HAIB","7.4718 bits → -5.93798 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","Antibody experiements showed that the C allele is a binding site, while the A allele is not. ","Concordant","Szalai et al. Single-nucleotide polymorphisms in the C-reactive protein (CRP) gene promoter that affect transcription factor binding, alter transcriptional activity, and associate with differences in baseline serum CRP level. 2005"]
[null,"rs34016643","NC_000008.11:g.118112204C>G","Human EXT1","GGCCCCGTGC → GGCCCGGTGC\nCGGCACGGGG → CGGCACCGGG","H1-hESC, HAIB","3.96767 bits → 0.571518 bit\n4.03378 bits → 2.17014 bits","The information contents of the binding sites decrease by 3.396152 bits and 1.86364 bits respectively, so USF1 binding decrease by 10.53 folds and 3.64 folds respectively. ","EMSA showed that no complex caused by USF1 binding appeared on the mutant allele, but ELISA showed that the binding capacity of the normal allele is higher than that of the mutant allele, and the binding capacity of the mutant allele is higher than that of the negative control.","Concordant","Jennes et al. Identifi cation and functional characterization of the human EXT1 promoter region. 2011"]
[null,"N/A","NC_000007.14:g.99795298insTGT","Human CYP3A4","AACCACATGT → CACAACATGT\nGAACATGTGG → GAACATGTTG","H1-hESC, HAIB","8.41412 bits → -6.78501 bits\n 3.14233 bits → -5.18667 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","EMSA demonstrated that the mutated allele with the insertion TGT is not a binding site.","Concordant","Matsumura et al. Identification of a Novel Polymorphic Enhancer of the Human CYP3A4 Gene. 2003"]
[null,"rs1800588","NC_000015.10:g.58431476C>T","Human HL","TGACACGGGG → TGACATGGGG","H1-hESC, HAIB","3.26215 bits → -2.70416 bits","The information content of the binding site becomes negative, so USF1 binding is abolished. ","EMSA showed that the the affinity of binding to the T allele is markedly lower than to the C allele, and the mutation decreased the binding by 4 folds.","Qualitatively concordant, quantitatively discordant","Botma et al. Hepatic lipase promoter activity is reduced by the C-480T and G-216A substitutions present in the common LIPC gene variant, and is increased by Upstream Stimulatory Factor. 2001"]
["USF2","rs2853542","NC_000018.10:g.657685G>C","Human TS","CCAAGTGGCG → CGAAGTGGCG","HeLa-S3, Stanford","4.00281 bits → -10.97261 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","EMSA showed that the mutation abolished USF2 binding.","Concordant","Mandola et al. A Novel Single Nucleotide Polymorphism within the 5 Tandem Repeat Polymorphism of the Thymidylate Synthase Gene Abolishes USF-1 Binding and Alters Transcriptional Activity. 2003"]
[null,"rs1135534 ","NC_000004.12:g.54228348C>A","Human PDGFRA","CCGCGTGGGT → CCGCTTGGGT","HeLa-S3, Stanford","2.0088 bits → -12.68823 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","EMSA demonstrated that the A allele is not a binding site.","Concordant","Toepoel et al. Haplotype-dependent binding of nuclear proteins to the promoter of the neural tube defects-associated platelet-derived growth factor alpha-receptor gene. 2005"]
[null,"rs2071592","NC_000006.11:g.31515340T>A","Human IKBL","CCACCTGCGT → CCACCAGCGT","HeLa-S3, Stanford","5.47018 bits → -7.52912 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","Supershift studies confirmed that USF2 binds to the T allele, but not the mutated A allele.","Concordant","Boodhoo et al. A promoter polymorphism in the central MHC gene, IKBL, influences the binding of transcription factors USF1 and E47 on disease-associated haplotypes. 2004"]
[null,"rs661204","NC_000011.10:g.69516215G>A","Human CCND1","CCCCATGATC → CCCCATAATC","HeLa-S3, Stanford","4.98264 bits → -10.00005 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","The A allele is not a genuine binding site.","Concordant","French et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. 2013"]
[null,"rs5050","NC_000001.11:g.230714140T>G","Human AGT","CATCGTGACC → CCTCGTGACC","HeLa-S3, Stanford","5.27288 bits → 11.1939 bits","The information content of the binding site increases by 5.92102 bits, so USF2 binding increases by 25.92102 ≈ 60.59 folds.","EMSA showed that the G allele is a stronger binding site than the T allele for USF.","Concordant","Zhao et al. Role of C/A Polymorphism at -20 on the Expression of Human Angiotensinogen Gene. 1999\nDickson et al. Upstream stimulatory factor is required for human angiotensinogen expression and differential regulation by the A-20C polymorphism. 2008"]
[null,"rs3093062","NC_000001.11:g.159714894C>T","Human CRP","GCACGTGGTA → GTACGTGGTA","HeLa-S3, Stanford","7.98824 bits → -6.98718 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","Antibody experiements showed that the C allele is a binding site, while the A allele is not. ","Concordant","Szalai et al. Single-nucleotide polymorphisms in the C-reactive protein (CRP) gene promoter that affect transcription factor binding, alter transcriptional activity, and associate with differences in baseline serum CRP level. 2005"]
[null,"rs34016643","NC_000008.11:g.118112204C>G","Human EXT1","CCCCGTGCCG → CCCGGTGCCG","HeLa-S3, Stanford","5.75402 bits → 3.87253 bits","The information content of the binding site decreases by 1.88149 bits, so USF2 binding decreases by 3.68 folds. ","EMSA showed that no complex caused by USF1 binding appeared on the mutant allele, but ELISA showed that the binding capacity of the normal allele is higher than that of the mutant allele, and the binding capacity of the mutant allele is higher than that of the negative control.","Concordant","Jennes et al. Identifi cation and functional characterization of the human EXT1 promoter region. 2011"]
[null,"N/A","NC_000007.14:g.99795298insTGT","Human CYP3A4","ACATGTGGTT → ACATGTTGTG\nCCACATGTTC → CAACATGTTC","HeLa-S3, Stanford","8.81847 bits → <0 bits\n 5.37825 bits → <0 bits","The information content of the binding site becomes negative, so USF2 binding is abolished. ","EMSA demonstrated that the mutated allele with the insertion TGT is not a binding site.","Concordant","Matsumura et al. Identification of a Novel Polymorphic Enhancer of the Human CYP3A4 Gene. 2003"]
[null,"rs1800588","NC_000015.10:g.58431476C>T","Human HL","CCCCGTGTCA → CCCCATGTCA","HeLa-S3, Stanford","5.9852 bits → 1.8386 bits","The information content of the binding site decreases by 4.1466 bits, so USF2 binding decreases by 24.1466 ≈ 17.71 folds.","EMSA showed that the the affinity of binding to the T allele is markedly lower than to the C allele.","Concordant","Botma et al. Hepatic lipase promoter activity is reduced by the C-480T and G-216A substitutions present in the common LIPC gene variant, and is increased by Upstream Stimulatory Factor. 2001"]
["YY1","rs3219018","NC_000001.11:g.161662856G>C","Human FCGR2B","TCCTGCATCACC → TCCTCCATCACC","GM12892, HAIB","(-7.10334 bits) → 8.27096 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ","In EMSA the DNA-protein complex is not at detectable level on the G allele.","Concordant","Su et al. A Promoter Haplotype of the Immunoreceptor Tyrosine-Based Inhibitory Motif-Bearing FcRIIb Alters Receptor Expression and Associates with Autoimmunity. 2004"]
[null,null,null,null,"GGTGATGCAGGA → GGTGATGGAGGA","K562, USC","(-6.95188 bits) → 6.72182 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ",null,"Concordant"]
[null,"rs28372960 ","NC_000005.10:g.150357401C>T","Human TCOF1","CCAGCCATCAGA → CTAGCCATCAGA","GM12892, HAIB","7.13267 bits → 3.66602 bits","The information content of the binding site increases by 3.46665 bits, so YY1 binding increases by 23.46665 ≈ 11.06 folds.","In the EMSA experiments, the complexes formed with the polymorphic probe were consistently less intense than the wild-type ones.","Concordant","Masotti et a. A functional SNP in the promoter region of TCOF1 is associated with reduced gene expression and YY1 DNA–protein interaction. 2005"]
[null,null,null,null,"TCTGATGGCTGG → TCTGATGGCTGA","K562, USC","5.00227 bits → 1.87633 bits","The information content of the binding site increases by 3.12594 bits, so YY1 binding increases by 23.12594 ≈ 8.73 folds.",null,"Concordant"]
[null,"rs3136674","NC_000017.11:g.34355597T>C","Human MCP4","TCAACCATTTTA → TCAACCATTCTA","GM12892, HAIB","6.53872 bits → 4.6181 bits","The information content of the binding site decreases by 1.92062 bits, so YY1 binding decreases by 21.92062 ≈ 3.79 folds.","EMSA showed that the T allele is stronger than the C allele.","Concordant","Kalayci et al. Monocyte Chemoattractant Protein-4 Core Promoter Genetic Variants Influence on YY-1 Affinity and Plasma Levels. 2003"]
[null,null,null,null,"TAAAATGGTTGA → TAGAATGGTTGA","K562, USC","6.88891 bits → 3.67569 bits","The information content of the binding site decreases by 3.21322 bits, so YY1 binding decreases by 23.21322 ≈ 9.27 folds.",null,"Concordant"]
[null,"rs7965413","NC_000012.12:g.6125723C>T","Human VWF","ACCACCGTGCCC → ACCACCATGCCC","GM12892, HAIB","(-9.2407 bits) → 5.724 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ","EMSA showed the lack of binding to the G allele, and that the substitution of the G nucleotide for an A is sufficient to create a new binding site.","Concordant","Costa et al. Human Endothelial Cell-derived Nuclear Proteins that Recognise Polymorphic DNA Elements in the von Willebrand Factor Gene Promoter Include YY1. 2001"]
[null,null,null,null,"GGGCACGGTGGT → GGGCATGGTGGT","K562, USC","(-4.31099 bits) → 4.29794 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ",null,"Concordant"]
[null,"rs7964777","NC_000012.12:g.6125905G>A","Human VWF","CACGCCATTCTC → CACGCCATTTTC","GM12892, HAIB","8.88127 bits → 10.8019 bits","The information content of the binding site increases by 1.92063 bits, so YY1 binding increases by 21.92063 ≈ 3.79 folds.","EMSA showed that the binding affinity of proteins to the T allele sequence is greater than that for the C allele variant.","Concordant","Costa et al. Human Endothelial Cell-derived Nuclear Proteins that Recognise Polymorphic DNA Elements in the von Willebrand Factor Gene Promoter Include YY1. 2001"]
[null,null,null,null,"GAGAATGGCGTG → GAAAATGGCGTG","K562, USC","7.10909 bits → 10.3223 bits","The information content of the binding site increases by 3.21321 bits, so YY1 binding increases by 23.21321 ≈ 9.27 folds.",null,"Concordant"]
[null,"rs10899353","NC_000011.10:g.77126506C>T","Human MYO7A","TAGGCCGTCTCT → TAGGCCATCTCT","GM12892, HAIB","(-7.69342 bits) → 7.27128 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ","EMSA, competition and supershift experiments showed that only the A allele can be bound by YY1.","Concordant","Street et al. A DNA Variant within the MYO7A Promoter Regulates YY1 Transcription Factor Binding and Gene Expression Serving as a Potential Dominant DFNA11 Auditory Genetic Modifier. 2011"]
[null,null,null,null,"AGAGACGGCCTA → AGAGATGGCCTA","K562, USC","(-0.77943 bit) → 7.8345 bits","The information content of the binding site becomes positive, so a new YY1 binding site is created. ",null,"Concordant"]
[null,"N/A","NC_000004.12:g.155910878G>T","Human TDO2","TCTGCCATTATT → TATGCCATTAT","GM12892, HAIB","8.13119 bits → 4.93219 bits","The information content of the binding site decreases by 3.199 bits, so YY1 binding decreases by 23.199 ≈ 9.18 folds.","EMSA showed that the T allele is a lower-affinity binding site.","Concordant","Vasiliev et al. Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. 1999"]
[null,null,null,null,"AATAATGGCAGA → AATAATGGCATA","K562, USC","7.72914 bits → 4.27982 bits","The information content of the binding site decreases by 3.44932 bits, so YY1 binding decreases by 23.44932 ≈ 10.92 folds.",null,"Concordant"]
[null,"N/A","NC_000005.10:g.112707523A>C","Human APC","TCCGCCATCTTG → TCCGCCATCTGG","GM12892, HAIB","14.5456 bits → 12.9136 bits","The information content of the binding site decreases by 1.632 bits, so YY1 binding decreases by 21.632 ≈ 3.10 folds.","EMSA showed that the point mutation disrupts YY1 binding.","Concordant","Li et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. 2016"]
[null,null,null,null,"CAAGATGGCGGA → CCAGATGGCGGA","K562, USC","16.3869 bits → 12.8731 bits","The information content of the binding site decreases by 3.5138 bits, so YY1 binding decreases by 23.5138 ≈ 11.42 folds.",null,"Concordant"]
[null,"N/A","NC_000005.10:g.112707526A>G","Human APC","TCCGCCATCTTG → TCCGCCACCTTG","GM12892, HAIB","14.5456 bits → 12.4305 bits","The information content of the binding site decreases by 2.1151 bits, so YY1 binding decreases by 22.1151 ≈ 4.33 folds.","EMSA showed that the point mutation disrupts YY1 binding.","Concordant","Li et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. 2016"]
[null,null,null,null,"CAAGATGGCGGA → CAAGGTGGCGGA","K562, USC","16.3869 bits → 8.48759 bits","The information content of the binding site decreases by 7.89931 bits, so YY1 binding decreases by 27.89931 ≈ 238.74 folds.",null,"Concordant"]
[null,"N/A","NC_000005.10:g.112707526A>T","Human APC","TCCGCCATCTTG → TCCGCCAACTTG","GM12892, HAIB","14.5456 bits → -0.52574 bit","The information content of the binding site becomes negative, so YY1 binding is abolished. ","EMSA showed that the point mutation disrupts YY1 binding.","Concordant","Li et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. 2016"]
[null,null,null,null,"CAAGATGGCGGA → CAAGTTGGCGGA","K562, USC","16.3869 bits → 4.59829 bits","The information content of the binding site decreases by 11.78861 bits, so YY1 binding decreases by 211.78861 ≈ 3537.73 folds.",null,"Concordant"]
[null,"N/A","NC_000005.10:g.112707527T>C","Human APC","TCCGCCATCTTG → TCCGCCGTCTTG","GM12892, HAIB","14.5456 bits → -0.4194 bit","The information content of the binding site becomes negative, so YY1 binding is abolished. ","EMSA showed that the point mutation disrupts YY1 binding.","Concordant","Li et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. 2016"]
[null,null,null,null,"CAAGATGGCGGA → CAAGACGGCGGA","K562, USC","16.3869 bits → 7.77297 bits","The information content of the binding site decreases by 8.61393 bits, so YY1 binding decreases by 28.61393 ≈ 391.79 folds.",null,"Concordant"]
[null,"N/A","NC_000005.10:g.112707528G>A","Human APC","TCCGCCATCTTG → TCCGCTATCTTG","GM12892, HAIB","14.5456 bits → -0.82906 bit","The information content of the binding site becomes negative, so YY1 binding is abolished. ","EMSA showed that the point mutation disrupts YY1 binding.","Concordant","Li et al. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. 2016"]
[null,null,null,null,"CAAGATGGCGGA → CAAGATAGCGGA","K562, USC","16.3869 bits → 2.70235 bits","The information content of the binding site decreases by 13.68455 bits, so YY1 binding decreases by 213.68455 ≈ 13166.19 folds.",null,"Concordant"]
[null,"N/A","NC_000004.12:g.155910875G>A","Human TDO2","TCTGCCATTATT → TCTGTCATTATT","GM12892, HAIB","8.13119 bits → -7.24311 bits","The information content of the binding site becomes negative, so YY1 binding is abolished. ","EMSA showed that the mutation abolishes YY1 binding.","Concordant","Vasiliev et al. Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. 1999"]
[null,null,null,null,"AATAATGGCAGA → AATAATGACATA","K562, USC","7.72914 bits → -5.94456 bits","The information content of the binding site becomes negative, so YY1 binding is abolished. ",null,"Concordant"]
[]
[null,"* Three categories of the comparison result:\nDiscordant: The directions of changes in binding site strengths predicted by the iPWMs differ from those observed in experiments (e.g. the iPWM predicts that TF binding will be strengthened, but experiments observed that binding was weakened).\nQualitatively concordant, quantitatively discordant: The directions are concordant, but the extents differ (e.g. TF binding is predicted to only be weakened, but experiments observed that binding was completely abolished).\nConcordant: The predictions of the iPWMs and the experimental observations are completely concordant.\nƚ The most significant changes in Ri values of binding sites predicted by the iPWMs are shown. The weaker, overlapping predicted sites on which the SNPs' effects are overshadowed by the most significant effects are not shown. The SNPs to which this situation occurs include rs4784227 and rs11986220 of FOXA1. Further information is available from the authors."]