Putative regulatory SNPs associated with AD and located in brain non-promoter regulatory regions

Columns description:

  • CHROM, POS, REF, ALT – chromosomal location of the SNP and its reference and alternative alleles,
  • AC, AF, AN – allele count, frequency and number in the analyzed cohort of Polish AD patients,
  • gnomAD genome NFE – frequency of the alternative allele in the non-Finnish European population according to the GnomAD genome resource,
  • Corrected p-value – p-value from the binomial test performed on the number of occurrences of the alternative allele in the analyzed cohort compared to expected frequency in NFE population, corrected for multiple-hypothesis testing with the Benjamini-Hochberg procedure,
  • TF motif, alleleDiff – putative transcription factor motif affected by the SNP according to the results from the motifbreakR tool and the difference in the motif scores obtained for the alternative and reference alleles,
  • Putative target gene – gene predicted to be influenced by the presence of the SNP in the regulatory region
  • TF motif hit plot – link to plots presenting the SNP in the context of TF binding motifs

Brief description of the project.

CHROM POS REF ALT AC AF AN gnomAD genome NFE Corrected p value TF motif alleleDiff Putative target gene TF motif hit plot
chr1 16913968 T A 3 0.065 46 0.0076 0.008741 INSM1_HUMAN.H11MO.0.C 4.234107 CROCC plot
chr1 16913970 A G 3 0.065 46 0.0076 0.008741 CTCFL_HUMAN.H11MO.0.A 4.217741 CROCC plot
chr1 24705404 T A 2 0.043 46 0 0 CEBPZ_HUMAN.H11MO.0.D -4.65396 CLIC4 plot
chr1 24705404 T A 2 0.043 46 0 0 FOXI1_HUMAN.H11MO.0.B -6.43775 CLIC4 plot
chr1 24705404 T A 2 0.043 46 0 0 IRF4_HUMAN.H11MO.0.A 4.168001 CLIC4 plot
chr1 1.62E+08 G C 2 0.043 46 0 0 E2F4_HUMAN.H11MO.0.A -3.46157 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 KLF9_HUMAN.H11MO.0.C -5.046 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 SP1_HUMAN.H11MO.0.A -3.48405 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 SP1_HUMAN.H11MO.1.A -4.98841 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 SP2_HUMAN.H11MO.1.B -5.78397 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 SP4_HUMAN.H11MO.0.A -3.32247 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 TFDP1_HUMAN.H11MO.0.C -3.19996 FCRLB plot
chr1 1.62E+08 G C 2 0.043 46 0 0 ZN740_HUMAN.H11MO.0.D 3.069822 FCRLB plot
chr1 1.65E+08 C A 2 0.043 46 0.0003 0.000286 HNF4A_HUMAN.H11MO.0.A 7.531016 PBX1 plot
chr1 1.65E+08 C A 2 0.043 46 0.0003 0.000286 MCR_HUMAN.H11MO.0.D 3.044522 PBX1 plot
chr1 2.24E+08 T A 2 0.045 44 8.05E-05 2.68E-05 IRF2_HUMAN.H11MO.0.A 3.36492 CAPN2 plot
chr1 2.24E+08 T A 2 0.045 44 8.05E-05 2.68E-05 ONEC2_HUMAN.H11MO.0.D -3.3673 CAPN2 plot
chr1 2.24E+08 T A 2 0.045 44 8.05E-05 2.68E-05 ONEC3_HUMAN.H11MO.0.D -9.40721 CAPN2 plot
chr1 2.31E+08 A C 2 0.043 46 0.0005 0.000692 RELB_HUMAN.H11MO.0.C 4.615121 FAM89A plot
chr1 2.31E+08 A C 2 0.043 46 0.0005 0.000692 REL_HUMAN.H11MO.0.B 4.94307 FAM89A plot
chr1 2.4E+08 A C 2 0.043 46 0.0013 0.003448 CPEB1_HUMAN.H11MO.0.D -4.09532 FMN2 plot
chr1 2.4E+08 A C 2 0.043 46 0.0013 0.003448 FOXJ3_HUMAN.H11MO.1.B 6.103154 FMN2 plot
chr1 2.4E+08 A C 2 0.043 46 0.0013 0.003448 FOXL1_HUMAN.H11MO.0.D 4.770456 FMN2 plot
chr10 78973767 G A 2 0.043 46 0.0025 0.009688 FLI1_HUMAN.H11MO.0.A 3.581945 ZMIZ1 plot
chr10 78973767 G A 2 0.043 46 0.0025 0.009688 IRF3_HUMAN.H11MO.0.B 3.147234 ZMIZ1 plot
chr10 86866412 T C 3 0.065 46 8.80E-05 6.79E-08 NFAC1_HUMAN.H11MO.0.B 4.161573 BMPR1A plot
chr10 86866412 T C 3 0.065 46 8.80E-05 6.79E-08 PRDM6_HUMAN.H11MO.0.C 5.932245 BMPR1A plot
chr10 97597450 C T 2 0.043 46 0.0011 0.002641 NKX23_HUMAN.H11MO.0.D 5.622317 HOGA1 plot
chr10 1.32E+08 C T 2 0.043 46 0.0021 0.007472 ZN549_HUMAN.H11MO.0.C 4.337552 JAKMIP3 plot
chr11 69212239 C T 3 0.065 46 0.0059 0.004909 HES1_HUMAN.H11MO.0.D -4.39445 MYEOV plot
chr11 69212239 C T 3 0.065 46 0.0059 0.004909 HEY2_HUMAN.H11MO.0.D -3.3673 MYEOV plot
chr12 4269215 C G 2 0.043 46 0.0001 3.92E-05 KLF12_HUMAN.H11MO.0.C -5.76142 CCND2 plot
chr12 4269215 C G 2 0.043 46 0.0001 3.92E-05 SP2_HUMAN.H11MO.1.B -3.79844 CCND2 plot
chr12 4269215 C G 2 0.043 46 0.0001 3.92E-05 ZN740_HUMAN.H11MO.0.D 4.11283 CCND2 plot
chr12 27225695 T C 3 0.088 34 0.0009 2.14E-05 NFAC1_HUMAN.H11MO.0.B 4.161573 STK38L plot
chr12 27225695 T C 3 0.088 34 0.0009 2.14E-05 PRDM6_HUMAN.H11MO.0.C 5.932245 STK38L plot
chr12 53591118 G A 2 0.043 46 0.0025 0.009688 TBX1_HUMAN.H11MO.0.D -4.96013 ATF7 plot
chr13 48110886 A G 4 0.087 46 0.0004 2.87E-08 FOXG1_HUMAN.H11MO.0.D 5.666427 MED4 plot
chr13 48110886 A G 4 0.087 46 0.0004 2.87E-08 PO3F3_HUMAN.H11MO.0.D 4.439509 MED4 plot
chr14 64693936 A G 2 0.043 46 0.0016 0.004822 BMAL1_HUMAN.H11MO.0.A 4.788133 PLEKHG3 plot
chr14 64693936 A G 2 0.043 46 0.0016 0.004822 MITF_HUMAN.H11MO.0.A 5.381943 PLEKHG3 plot
chr14 64693936 A G 2 0.043 46 0.0016 0.004822 TFE3_HUMAN.H11MO.0.B 3.230403 PLEKHG3 plot
chr14 64693936 A G 2 0.043 46 0.0016 0.004822 TFEB_HUMAN.H11MO.0.C 6.944087 PLEKHG3 plot
chr14 64693936 A G 2 0.043 46 0.0016 0.004822 USF1_HUMAN.H11MO.0.A 3.549943 PLEKHG3 plot
chr15 77808233 G C 2 0.043 46 0 0 SP1_HUMAN.H11MO.1.A 4.838112 LINGO1 plot
chr15 1E+08 T C 3 0.065 46 0.0004 5.12E-06 PRDM6_HUMAN.H11MO.0.C 3.935596 ADAMTS17 plot
chr16 68497 C T 3 0.065 46 0.0042 0.002224 SALL4_HUMAN.H11MO.0.B -5.02439 RHBDF1 plot
chr16 68497 C T 3 0.065 46 0.0042 0.002224 TBX15_HUMAN.H11MO.0.D -4.41891 RHBDF1 plot
chr17 17032283 G T 2 0.043 46 0.0009 0.001869 ETV1_HUMAN.H11MO.0.A -7.6014 MPRIP plot
chr17 59380388 G C 3 0.065 46 0.0024 0.000563 ZN770_HUMAN.H11MO.1.C -5.96152 YPEL2 plot
chr17 66518319 T G 2 0.043 46 0.0004 0.000477 CEBPZ_HUMAN.H11MO.0.D 4.65396 PRKCA plot
chr17 66518319 T G 2 0.043 46 0.0004 0.000477 FOXI1_HUMAN.H11MO.0.B 4.821893 PRKCA plot
chr17 66518319 T G 2 0.043 46 0.0004 0.000477 PBX3_HUMAN.H11MO.1.A 7.599401 PRKCA plot
chr17 75826405 T G 2 0.043 46 0 0 ZEB1_HUMAN.H11MO.0.A -4.85503 UNC13D plot
chr18 13576449 G A 2 0.043 46 0.0003 0.000286 CPEB1_HUMAN.H11MO.0.D 3.137671 LDLRAD4 plot
chr18 13576449 G A 2 0.043 46 0.0003 0.000286 IRF1_HUMAN.H11MO.0.A 5.633416 LDLRAD4 plot
chr18 13576449 G A 2 0.043 46 0.0003 0.000286 IRF2_HUMAN.H11MO.0.A 5.394132 LDLRAD4 plot
chr18 13576449 G A 2 0.043 46 0.0003 0.000286 IRF8_HUMAN.H11MO.0.B 5.024119 LDLRAD4 plot
chr18 13576449 G A 2 0.043 46 0.0003 0.000286 MNX1_HUMAN.H11MO.0.D 4.043346 LDLRAD4 plot
chr19 2167742 T C 2 0.043 46 0 0 NFAC1_HUMAN.H11MO.0.B 4.161573 DOT1L plot
chr19 2167742 T C 2 0.043 46 0 0 PRDM6_HUMAN.H11MO.0.C 5.932245 DOT1L plot
chr19 6515973 G A 2 0.045 44 0.0007 0.001167 CPEB1_HUMAN.H11MO.0.D 3.895 TUBB4A plot
chr19 7224268 C A 6 0.13 46 7.91E-05 2.10E-17 MYNN_HUMAN.H11MO.0.D 4.39154 INSR plot
chr2 8684545 A C 2 0.043 46 0.0005 0.000692 KLF16_HUMAN.H11MO.0.D 3.180565 ID2 plot
chr2 8684545 A C 2 0.043 46 0.0005 0.000692 PROX1_HUMAN.H11MO.0.D 3.942093 ID2 plot
chr20 33693104 G A 2 0.043 46 0.0002 0.00014 CPEB1_HUMAN.H11MO.0.D 4.28671 E2F1 plot
chr20 33693104 G A 2 0.043 46 0.0002 0.00014 FOXL1_HUMAN.H11MO.0.D 6.658941 E2F1 plot
chr20 33693104 G A 2 0.043 46 0.0002 0.00014 SRY_HUMAN.H11MO.0.B 4.333361 E2F1 plot
chr20 33693104 G A 2 0.043 46 0.0002 0.00014 ZIM3_HUMAN.H11MO.0.C -7.54168 E2F1 plot
chr21 45554469 C A 2 0.045 44 0 0 ZN740_HUMAN.H11MO.0.D -3.702 SLC19A1 plot
chr22 30872281 T C 3 0.065 46 0.0044 0.002501 NKX61_HUMAN.H11MO.0.B -3.23449 OSBP2 plot
chr3 73636559 G T 2 0.043 46 0.0009 0.001869 FOXJ2_HUMAN.H11MO.0.C 3.471966 PDZRN3 plot
chr3 73636559 G T 2 0.043 46 0.0009 0.001869 FOXL1_HUMAN.H11MO.0.D 8.474077 PDZRN3 plot
chr3 1.26E+08 T G 2 0.043 46 0.0022 0.008028 CPEB1_HUMAN.H11MO.0.D -3.85414 OSBPL11 plot
chr3 1.26E+08 T G 2 0.043 46 0.0022 0.008028 FOXJ3_HUMAN.H11MO.1.B 7.113226 OSBPL11 plot
chr3 1.26E+08 T G 2 0.043 46 0.0022 0.008028 FOXL1_HUMAN.H11MO.0.D -3.80091 OSBPL11 plot
chr3 1.26E+08 T G 2 0.043 46 0.0022 0.008028 SRY_HUMAN.H11MO.0.B 3.776585 OSBPL11 plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 E2F4_HUMAN.H11MO.0.A 7.51186 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 KLF13_HUMAN.H11MO.0.D 10.31986 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 KLF14_HUMAN.H11MO.0.D 4.131432 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 KLF1_HUMAN.H11MO.0.A 5.371671 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 KLF3_HUMAN.H11MO.0.B 7.007583 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 MAZ_HUMAN.H11MO.1.A 6.378426 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 SP1_HUMAN.H11MO.1.A 7.390799 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 SP2_HUMAN.H11MO.0.A 3.926514 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 SP2_HUMAN.H11MO.1.B 7.340187 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 SP4_HUMAN.H11MO.1.A 4.200908 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 WT1_HUMAN.H11MO.0.C 3.496508 CENPE plot
chr4 1.03E+08 G C 2 0.045 44 0.0006 0.000901 ZN770_HUMAN.H11MO.0.C -3.51124 CENPE plot
chr4 1.13E+08 G T 2 0.048 42 0 0 NFAC1_HUMAN.H11MO.0.B 4.327042 ANK2 plot
chr4 1.13E+08 G T 2 0.048 42 0 0 PRDM6_HUMAN.H11MO.0.C 4.08266 ANK2 plot
chr4 1.13E+08 G T 2 0.048 42 0 0 ZFP82_HUMAN.H11MO.0.C 3.615321 ANK2 plot
chr4 1.13E+08 C T 2 0.048 42 0 0 FUBP1_HUMAN.H11MO.0.D 5.169894 ANK2 plot
chr4 1.69E+08 G A 2 0.043 46 0.0007 0.001228 NR2E1_HUMAN.H11MO.0.D -5.51745 PALLD plot
chr4 1.69E+08 G A 2 0.043 46 0.0007 0.001228 ZN586_HUMAN.H11MO.0.C -4.15942 PALLD plot
chr5 1.08E+08 G T 5 0.114 44 0.0022 3.19E-07 FUBP1_HUMAN.H11MO.0.D -3.79674 EFNA5 plot
chr5 1.08E+08 G T 5 0.114 44 0.0022 3.19E-07 HXC6_HUMAN.H11MO.0.D 3.367296 EFNA5 plot
chr5 1.08E+08 G T 5 0.114 44 0.0022 3.19E-07 LMX1A_HUMAN.H11MO.0.D 4.484397 EFNA5 plot
chr5 1.08E+08 G T 5 0.114 44 0.0022 3.19E-07 ONEC2_HUMAN.H11MO.0.D 3.367296 EFNA5 plot
chr5 1.4E+08 G A 2 0.043 46 0.0023 0.008603 ZN708_HUMAN.H11MO.1.D -4.34381 NRG2 plot
chr6 37561432 G A 2 0.043 46 0.0019 0.006385 SMAD2_HUMAN.H11MO.0.A -3.03956 CCDC167 plot
chr7 218574 T A 2 0.043 46 0.0011 0.002641 ZN121_HUMAN.H11MO.0.C 3.395521 FAM20C plot
chr7 55129169 G C 2 0.043 46 0.0005 0.000692 PAX2_HUMAN.H11MO.0.D 4.828314 EGFR plot
chr7 1.55E+08 T C 2 0.043 46 0.0018 0.005839 NFIC_HUMAN.H11MO.0.A -3.83388 EN2 plot
chr7 1.55E+08 T C 2 0.043 46 0.0018 0.005839 ZN586_HUMAN.H11MO.0.C -3.91148 EN2 plot
chr8 1E+08 C T 2 0.043 46 0.0001 3.92E-05 NFIC_HUMAN.H11MO.1.A -7.5606 RNF19A plot
chr9 18446848 G T 2 0.043 46 0.0013 0.003448 SOX10_HUMAN.H11MO.0.B 4.303524 ADAMTSL1 plot
chr9 95463010 G T 2 0.043 46 0.0007 0.001228 NFAT5_HUMAN.H11MO.0.D 4.345881 PTCH1 plot
chrX 53072145 A G 2 0.043 46 0.0022 0.008028 KLF9_HUMAN.H11MO.0.C 6.924612 TSPYL2 plot
chrX 53072145 A G 2 0.043 46 0.0022 0.008028 MZF1_HUMAN.H11MO.0.B -5.39211 TSPYL2 plot
chrX 53072145 A G 2 0.043 46 0.0022 0.008028 ZN148_HUMAN.H11MO.0.D 4.919981 TSPYL2 plot

These results have been obtained within the “Identification of regulatory non-coding variants associated with neurodegenerative disorders based on targeted sequencing of open chromatin regions” project funded by the Foundation for Polish Science (within the POWROTY/REINTEGRATION programme co-financed by the European Union under the European Regional Development Fund, POIR.04.04.00-00-3E86/17-00).

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