JOB ID = TC_db138thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 6421 SNPs in input data, 316 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 8.34 SNPs per million bases in TSS regions, compared with 2.03 SNPs per million bases genome-wide. 519 TSS regions were hit, in 128 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
Hepatocyte1.6e-170
liver_adult_pool16.8e-120
Prostate_Epithelial_Cells7.6e-070
liver_fetal_pool14.8e-060
intestinal_epithelial_cells_polarised0.000130
colon_adult_pool10.00420.0029
HES3GFP_Embryonic_Stem_cells_cardiomyocytic_induction_day124.1e-060.0037
HES3GFP_Embryonic_Stem_cells_cardiomyocytic_induction_day050.000970.0038
Renal_Proximal_Tubular_Epithelial_Cell0.0410.0038
Renal_Mesangial_Cells0.0240.0043
H9_Embryoid_body_cells_melanocytic_induction_day120.00160.0047
kidney_fetal_pool10.0190.0072
HES3GFP_Embryonic_Stem_cells_cardiomyocytic_induction_day020.00190.011
HES3GFP_Embryonic_Stem_cells_cardiomyocytic_induction_day080.00570.038
HES3GFP_Embryonic_Stem_cells_cardiomyocytic_induction_day070.00230.04
Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p58@APOB [rs533617]0.7400.0
p@chr7:44581054..44581057,+ [rs41279633, rs17655652]0.6800.0
+ linkage disequilibrium:rs17655652:rs732797 D'=0.92; r2=0.4. p@chr7:44646674..44646689,+ [rs732797]0.2610.3
p6@HNF1A-AS1 [rs1169286]0.6500.0
+ linkage disequilibrium:rs1169286:rs2258287 D'=0.68; r2=0.39. p1@C12orf43 [rs2258287]0.1610.61
p2@ENST00000518619 [rs11774381, rs9987289, rs4841132]0.6400.0
+ linkage disequilibrium:rs9987289:rs7357361 D'=1.0; r2=0.57. enhancer@chr8:9219931-9220273 [rs7357361]
rs4841132:rs7357361 D'=1.0; r2=0.57. enhancer@chr8:9219931-9220273 [rs7357361]
0.2610.3
p3@LIPC [rs2070895]0.6100.0
p5@ABCA1 [rs1800978]0.5800.0
p3@ABCG5 [rs11887534]0.5400.0
+ linkage disequilibrium:rs11887534:rs13395550 D'=0.25; r2=0.06. enhancer@chr2:44007303-44007575 [rs13395550]0.0810.81
p1@GPN1 [rs3749147]0.5400.0
+ linkage disequilibrium:same SNP, different promoter: p1@CCDC121 [rs3749147]0.0610.87
enhancer@chr6:30731311-30731508 [rs3095338]0.5200.0
+ linkage disequilibrium:rs3095338:rs8233 D'=0.91; r2=0.62. p@chr6:30692851..30692934,+ [rs8233]0.1710.58
p3@HAVCR1 [rs67960962]0.5100.0
+ linkage disequilibrium:rs67960962:rs6882076 D'=0.83; r2=0.31. p1@TIMD4 [rs6882076]0.0610.87
p1@APOA5 [rs651821]0.5100.0
+ linkage disequilibrium:rs651821:rs689243 D'=1.0; r2=0.21. enhancer@chr11:116722234-116722744 [rs689243]0.011.0
p1@ENST00000447070 [rs6760828]0.500.0
+ linkage disequilibrium:rs6760828:rs4665963 D'=0.77; r2=0.31. p@chr2:27528919..27528940,+ [rs4665963]0.3310.12
p@chr16:72075048..72075055,- [rs9932951]0.480.0170.0
+ linkage disequilibrium:rs9932951:rs3213422 D'=0.29; r2=0.08. p1@DHODH [rs34270657, rs3213422]0.430.170.01
p1@SPTY2D1 [rs7943121]0.480.0170.0
p@chr19:19616795..19616800,+ [rs1063966]0.480.0170.0
+ linkage disequilibrium:rs1063966:rs73004933 D'=1.0; r2=0.19. p@chr19:19675738..19675742,- [rs73004933]0.3710.06
+ linkage disequilibrium:rs1063966:rs4808967 D'=1.0; r2=1.0. p@chr19:19640454..19640461,+ [rs4808967]0.1110.76
p@chr6:26500524..26500540,+ [rs13194984]0.470.0170.0
p3@SLC22A1 [rs12208357]0.460.0670.0
p6@RBM39 [rs2425090]0.460.0670.0
p16@HLA-DQA1 [rs9272775]0.440.130.01
p37@CFB [rs2072633]0.440.130.01
p@chr2:27975692..27975750,+ [rs6547796]0.430.170.01
+ linkage disequilibrium:rs6547796:rs13013484 D'=1.0; r2=0.9. p@chr2:27988549..27988557,- [rs13013484]0.1710.58
chr6:160770176..160770186,- [rs474513, rs539298]0.430.220.01
p7@PCSK9 [rs11591147]0.420.370.02
p@chr19:45411878..45411884,- [rs7412]0.410.570.02
p1@FEN1 [rs412334, rs174538]0.40.860.03
+ linkage disequilibrium:same SNP, different promoter: p4@C11orf10 [rs412334]
rs174538:rs412334 D'=1.0; r2=0.07. p4@C11orf10 [rs412334]
0.3510.07
p1@SPATC1 [rs6985603]0.3910.04
p@chr18:47176875..47176889,+ [rs4939886, rs4939887, rs4939888]0.3910.04
p1@NAT2 [rs4646246]0.3810.05
p@chr9:136154265..136154271,- [rs579459, rs649129]0.3810.05
+ linkage disequilibrium:rs579459:rs568203 D'=1.0; r2=0.1. p@chr9:136151396..136151407,- [rs568203]
rs649129:rs568203 D'=1.0; r2=0.1. p@chr9:136151396..136151407,- [rs568203]
0.2610.3
enhancer@chr8:126446642-126447323 [rs2385114]0.3710.06
p@chr1:63112277..63112278,+ [rs1168085]0.3710.06
p3@NSMAF [rs2279460]0.3710.06
enhancer@chr20:34127589-34128004 [rs2104417]0.3610.07
p13@UGT1A6 [rs2070959]0.3610.07
+ linkage disequilibrium:rs2070959:rs17864701 D'=0.92; r2=0.8. p2@DNAJB3 [rs17864701]0.2510.3
p2@SPC24 [rs892114, rs7251031]0.3610.07
enhancer@chr5:74805918-74806308 [rs5744533]0.3610.07
p1@AK311221 [rs9469089]0.3510.09
+ linkage disequilibrium:rs9469089:rs3134931 D'=0.49; r2=0.14. p@chr6:32190527..32190536,- [rs3134931]0.0910.81
p@chr16:68114139..68114174,+ [rs7188085]0.3410.1
p@chr1:221054751..221054771,- [rs17597773]0.3410.1
p1@POC5 [rs2291630]0.3310.11
+ linkage disequilibrium:rs2291630:rs34358 D'=1.0; r2=0.47. p@chr5:74965139..74965165,+ [rs34358]0.2410.37
+ linkage disequilibrium:rs2291630:rs2047059 D'=1.0; r2=0.64. p2@POC5 [rs2047059]0.1710.58
+ linkage disequilibrium:rs2291630:rs7715806 D'=0.95; r2=0.39. enhancer@chr5:75034241-75034569 [rs7715806]0.1610.63
p2@LY6G6C [rs805292]0.3310.11
p@chr6:16131425..16131449,+ [rs2235215]0.3310.11
p@chr2:136594310..136594317,+ [rs2236783]0.3310.12
+ linkage disequilibrium:rs2236783:rs1438307 D'=0.94; r2=0.85. p2@UBXN4 [rs1438307]0.1310.74
enhancer@chr6:135435494-135435847 [rs9483788]0.3210.13
p1@HLA-DRB9 [rs13191565]0.3110.17
p1@USP1 [rs646179]0.310.2
enhancer@chr19:45242034-45242469 [rs1531517]0.2810.23
+ linkage disequilibrium:rs1531517:rs10422182 D'=0.62; r2=0.22. p@chr19:45159154..45159158,+ [rs10422182]0.0910.81
p@chr19:10961151..10961183,+ [rs11085749]0.2810.25
+ linkage disequilibrium:rs11085749:rs2288842 D'=1.0; r2=0.61. chr19:11031515..11031547,+ [rs2288842]0.2310.38
p12@PLCG1 [rs6124323]0.2810.25
enhancer@chr10:17254796-17255338 [rs7080366]0.2710.26
p2@LPIN3 [rs6029636]0.2610.29
p1@ENST00000408001 [rs2764205]0.2510.3
+ linkage disequilibrium:rs2764205:rs3800457 D'=1.0; r2=0.96. enhancer@chr6:34663389-34663600 [rs3800457]0.0810.81
enhancer@chr16:56985400-56985562 [rs12448528, rs72786786]0.2510.3
p@chr9:15298766..15298791,+ [rs675849]0.2410.36
p@chr1:63266602..63266609,- [rs11208033, rs10493328, rs4409690]0.2310.38
+ 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]
0.0810.81
p4@SH2B3 [rs739496]0.2310.38
p3@C6orf10 [rs6913309, rs2050189]0.2110.45
p@chr2:113841162..113841225,+ [rs6734238]0.2110.45
p1@FRK [rs1999929]0.2110.45
p@chr16:71934252..71934256,+ [rs4788576]0.210.48
enhancer@chr2:136816831-136817220 [rs749873]0.1910.55
+ linkage disequilibrium:rs749873:rs309137 D'=0.86; r2=0.52. enhancer@chr2:136765824-136766130 [rs309137]0.1210.76
+ linkage disequilibrium:rs749873:rs6714750 D'=1.0; r2=0.55. enhancer@chr2:136783030-136783335 [rs6714750]0.110.79
p4@HMGCR [rs3761740]0.1910.56
enhancer@chr19:46018095-46018753 [rs7255743]0.1810.56
p6@UBASH3B [rs7127978]0.1810.58
enhancer@chr11:48004294-48004631 [rs7946766]0.1710.58
chr20:39634184..39634189,- [rs1000410]0.1710.58
p@chr2:203131655..203131667,- [rs7581542]0.1710.58
chr11:118486256..118486298,+ [rs11603023]0.1710.58
p@chr11:116980715..116980720,- [rs10892074]0.1510.66
+ linkage disequilibrium:rs10892074:rs508487 D'=1.0; r2=0.09. p@chr11:117075245..117075293,- [rs508487]0.0210.96
enhancer@chr16:31129616-31130225 [rs9925964]0.1510.66
p@chr12:112212004..112212016,+ [rs2238151]0.1410.67
p4@GSTM4 [rs1010167]0.1410.67
p@chr17:76377571..76377602,- [rs4082919]0.1310.74
p@chr1:109784420..109784424,+ [rs688386]0.1210.75
p@chr4:88057279..88057283,+ [rs1408]0.1210.76
p6@SYN2 [rs3773364]0.1110.78
chr19:10742301..10742328,+ [rs2288904, rs1560711]0.1110.78
chr6:31808499..31808514,+ [rs599707]0.110.78
p1@ERGIC2 [rs2278093]0.110.8
p2@HLA-L [rs9391806]0.0910.81
p6@PHC1 [rs3809218]0.0910.81
p@chr5:74964235..74964256,+ [rs7715739, rs369034591]0.0910.81
p@chr17:37405559..37405561,- [rs2061342]0.0810.81
p@chr2:28124429..28124474,+ [rs10177845]0.0810.81
enhancer@chr22:35708559-35708961 [rs138774]0.0810.82
p@chr2:216286896..216286912,- [rs1250248]0.0710.87
p@chr2:135893438..135893485,+ [rs10445686]0.0610.87
enhancer@chr17:37836315-37836462 [rs9303274]0.0610.87
+ linkage disequilibrium:rs9303274:rs1053651 D'=0.91; r2=0.65. p@chr17:37822585..37822591,+ [rs1053651]0.0110.99
enhancer@chr15:58712788-58712944 [rs11854624]0.0610.87
+ linkage disequilibrium:rs11854624:rs17821310 D'=1.0; r2=0.86. p1@LIPC [rs17821310]0.0110.99
enhancer@chr8:59311673-59312115 [rs1030431]0.0510.9
p@chr20:34001017..34001019,- [rs6087704]0.0510.9
enhancer@chr11:61713558-61713889 [rs1534842]0.0410.91
p1@GPR61 [rs552101]0.0410.91
p@chr3:12704956..12704973,- [rs904453]0.0410.92
p2@CU690121 [rs12225230]0.0410.92
enhancer@chr1:92668364-92668570 [rs3131816]0.0310.96
p2@PACSIN1 [rs11758326]0.0110.98
p1@ATXN2 [rs695871]0.011.0