JOB ID = TG_db138-1thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 4863 SNPs in input data, 254 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 7.02 SNPs per million bases in TSS regions, compared with 1.54 SNPs per million bases genome-wide. 437 TSS regions were hit, in 97 distinct regions. Results are shown below for coexpression within the input set compared with 100 pre-mapping (genome-wide) permutations. Download full results file here.

Please cite: Baillie JK et al. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. https://doi.org/10.1101/095349.

Link threshold (-log10 p):

0 4

Significantly coexpressed regulatory regions

Other regulatory regions containing a variant

CircosPlot

Circular (Circos) plot of co-expression links between different locations on the genome. The coloured track shows an end-to-end concatenated view of the human chromosomes. Links depict an association between two SNP clusters and are coloured according to -log10(p)(line colour indicates -log10(p): red>3, blue>2, green>1.5).

QQ plot

Quantile-quantile plot showing observed and expected co-expression scores. Expected co-expression scores are derived from circular permuted subsets of regulatory regions (post-mapping permutations; black circles) or SNPs chosen by circular permutations against the background of all SNPs genotyped in each study.

Cell typeRRA pFDR
small_intestine_adult_pool12.4e-060
colon_adult_pool10.000990
small_intestine_fetal0.00360
duodenum_fetal_donor1_tech3.2e-050.015
Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p67@APOB [rs676210]0.6300.0
p@chr2:165603346..165603357,- [rs10178921]0.560.0180.01
p@chr2:27528919..27528940,+ [rs4665963]0.530.0360.01
+ linkage disequilibrium:rs4665963:rs11684134 D'=0.8; r2=0.3. p1@LOC100505624 [rs11684134]0.420.290.02
p@chr7:73106975..73106980,+ [rs2293490]0.520.0360.01
p32@ACSL5 [rs11195943]0.510.0360.01
p@chr11:116691448..116691464,- [rs5110, rs675]0.50.0360.01
p@chr19:45411878..45411884,- [rs7412]0.50.0540.01
p1@ZSWIM1 [rs3746497]0.50.0540.01
p@chr7:17287199..17287204,+ [rs6968554]0.490.0540.01
p@chr6:31254912..31254928,- [rs9468920]0.480.0540.01
enhancer@chr7:72939749-72940060 [rs80189144]0.480.0720.01
p@chr12:124433988..124434017,- [rs2178663]0.460.110.01
p1@BAG6 [rs3117582]0.450.130.01
p@chr6:52617751..52617757,- [rs2180314]0.440.140.01
p@chr19:7184803..7184814,- [rs17253937]0.430.240.02
p1@ENST00000518619 [rs17149760]0.420.250.02
p@chr20:44640866..44640875,- [rs3918256]0.40.470.03
p@chr4:88057279..88057283,+ [rs1408]0.40.510.03
+ linkage disequilibrium:rs1408:rs3755980 D'=1.0; r2=0.14. p@chr4:88042092..88042099,- [rs3755980]0.1810.45
p1@ENST00000448198, p1@ENST00000455328 [rs3916765]0.380.980.05
enhancer@chr19:19483893-19484092 [rs59148799]0.3710.05
p1@NSUN5 [rs1880948]0.3710.05
chr6:30798448..30798455,- [rs1264347]0.3710.05
+ linkage disequilibrium:rs1264347:rs886422 D'=1.0; r2=1.0. p23@DDR1 [rs886422]0.0510.82
p2@LIPC [rs2070895]0.3710.05
p@chr19:45487536..45487571,+ [rs16979600]0.3610.06
+ linkage disequilibrium:rs16979600:rs3760629 D'=1.0; r2=0.05. p3@CLPTM1 [rs3760629]0.1310.61
p2@LY6G6C [rs805292]0.3610.06
p@chr4:87873088..87873092,+ [rs1992876]0.3510.07
p@chr8:19782798..19782817,- [rs28522139]0.3410.08
p@chr8:11396776..11396795,+ [rs2409784]0.3310.09
chr2:28203328..28203338,+ [rs898031]0.3310.09
+ linkage disequilibrium:rs898031:rs2305929 D'=1.0; r2=0.1. p@chr2:28114209..28114224,+ [rs2305929]0.110.68
p1@HAX1 [rs11556341]0.3310.11
+ linkage disequilibrium:same SNP, different promoter: p@chr1:154244875..154244901,- [rs11556341]0.1410.61
p@chr2:28634997..28635008,+ [rs12624279]0.3210.11
p1@ZNF646 [rs2303222]0.3210.11
p2@F2 [rs2070852]0.310.15
+ linkage disequilibrium:rs2070852:rs7932354 D'=1.0; r2=1.0. p1@ARHGAP1 [rs7932354]0.1310.61
enhancer@chr15:58712788-58712944 [rs11854624]0.310.16
+ linkage disequilibrium:rs11854624:rs17821310 D'=1.0; r2=0.86. p1@LIPC [rs17821310]0.110.68
p1@ENST00000519197 [rs28597716]0.2910.18
enhancer@chr11:47109490-47109615 [rs4319472]0.2810.2
p1@NAT2 [rs4646246]0.2810.21
enhancer@chr16:56985400-56985562 [rs72786786, rs12448528]0.2710.23
p@chr6:33153425..33153432,- [rs9277934]0.2710.23
+ linkage disequilibrium:rs9277934:rs2076311 D'=1.0; r2=1.0. p@chr6:33145331..33145378,- [rs2076311]0.0710.79
enhancer@chr8:11032163-11032532 [rs6986032]0.2710.23
p@chr1:62928606..62928608,+ [rs998403]0.2710.23
p@chr1:63112277..63112278,+ [rs1168085]0.2610.23
p@chr6:32411003..32411021,- [rs3135391]0.2610.25
p11@SIDT2 [rs474339]0.2510.26
+ linkage disequilibrium:rs474339:rs10892074 D'=1.0; r2=0.25. p@chr11:116980715..116980720,- [rs10892074]0.1410.61
+ linkage disequilibrium:rs474339:rs508487 D'=1.0; r2=0.37. p@chr11:117075245..117075293,- [rs508487]0.0510.82
p@chr19:19640431..19640450,+ [rs4808967]0.2410.3
+ linkage disequilibrium:rs4808967:rs1063966 D'=1.0; r2=1.0. p@chr19:19616795..19616800,+ [rs1063966]0.1710.48
p@chr8:19830089..19830095,+ [rs1569209]0.2410.31
p1@TIMD4 [rs6882076]0.2310.31
enhancer@chr11:116722234-116722744 [rs689243]0.2310.32
p@chr11:47303410..47303414,+ [rs326217]0.2210.34
p@chr8:126442070..126442090,- [rs4871594]0.2110.37
p@chr2:27975692..27975750,+ [rs6547796]0.2110.37
p@chr1:63266602..63266609,- [rs11208033, rs10493328, rs4409690]0.2110.37
+ linkage disequilibrium:rs11208033:rs12122434 D'=1.0; r2=0.22. p@chr1:63261897..63261900,+ [rs12122434]
rs10493328:rs12122434 D'=1.0; r2=0.22. p@chr1:63261897..63261900,+ [rs12122434]
rs4409690:rs12122434 D'=1.0; r2=0.22. p@chr1:63261897..63261900,+ [rs12122434]
0.1910.42
p3@FADS2 [rs968567]0.210.42
chr6:31808499..31808514,+ [rs599707]0.1910.42
enhancer@chr10:65274637-65275000 [rs10761779]0.1910.45
chr6:160770176..160770186,- [rs474513, rs539298]0.1810.48
enhancer@chr6:32913033-32913520 [rs1480380]0.1610.52
enhancer@chr2:227020272-227020467 [rs13404263]0.1610.52
p1@HLA-DQB1 [rs3891175]0.1510.56
enhancer@chr3:52531917-52532418 [rs13326165]0.1510.59
p9@IFT172 [rs780104, rs79740025, rs6734392]0.1310.61
p@chr10:65121474..65121480,- [rs12355784]0.1310.61
enhancer@chr1:230279464-230279771 [rs4846905]0.1310.61
+ linkage disequilibrium:rs4846905:rs7551742 D'=0.93; r2=0.83. enhancer@chr1:230289705-230290142 [rs7551742]0.0810.77
enhancer@chr2:28319174-28319559 [rs7568903]0.1310.61
chr6:32148013..32148032,+ [rs3134943]0.1310.61
+ linkage disequilibrium:rs3134943:rs3134931 D'=1.0; r2=0.08. p@chr6:32190527..32190536,- [rs3134931]0.0710.79
+ linkage disequilibrium:rs3134943:rs3131283 D'=1.0; r2=0.92. p3@PRRT1 [rs3131283]0.0310.88
p3@CPEB4 [rs55946741]0.1110.67
p1@ENST00000451079 [rs12442297]0.1110.68
p@chr16:72108093..72108100,+ [rs2000999]0.1110.68
enhancer@chr8:19518773-19518959 [rs4921664]0.0910.74
+ linkage disequilibrium:rs4921664:rs7001715 D'=1.0; r2=0.66. p@chr8:19507328..19507329,- [rs7001715]0.0510.82
p@chr22:38572651..38572665,+ [rs133017]0.0810.77
p@chr16:81610493..81610521,+ [rs11642655]0.0710.79
enhancer@chr8:59311673-59312115 [rs1030431]0.0710.79
enhancer@chr15:44289112-44289501 [rs6493092]0.0710.79
enhancer@chr3:170695585-170695919 [rs7635100]0.0510.82
enhancer@chr11:61746281-61746413 [rs10792320]0.0510.83
p@chr2:28524175..28524215,+ [rs12621972]0.0410.86
enhancer@chr6:127481688-127482073 [rs9491700]0.0410.86
enhancer@chr2:227172292-227172683 [rs2713556]0.0210.91
enhancer@chr15:44431053-44431468 [rs2555389]0.0110.94
p8@MAPK10 [rs2869433]0.011.0
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