JOB ID = HDL_db138-1thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 5410 SNPs in input data, 260 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 7.23 SNPs per million bases in TSS regions, compared with 1.71 SNPs per million bases genome-wide. 450 TSS regions were hit, in 101 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
Hepatocyte4.3e-140
liver_adult_pool13.1e-100
mesenchymalstemcells(adiposederived)adipogenicinduction_day080.000140
mesenchymalstemcells(adiposederived)adipogenicinduction_day140.000180.0064
Adipocyte_differentiation_day080.00370.0064
Adipocyte_subcutaneous0.00620.0064
liver_fetal_pool10.00510.027
mesenchymalstemcells(adiposederived)adipogenicinduction_undifferentiatedcontrol0.0280.042
Adipocyte_differentiation_day120.0280.042
macLPS_00hr00min0.0230.042
macLPS_22hr0.0450.049
Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p@chr9:107669326..107669336,+ [rs4100654, rs13284054]0.7100.0
p2@ENST00000518619 [rs9987289, rs4841132]0.6700.0
+ 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]
0.110.76
chr11:47281010..47281020,+ [rs11039155]0.6400.0
p13@BC172787 [rs693]0.6400.0
p1@SLC17A3 [rs13198474]0.600.0
p@chr18:47176875..47176889,+ [rs4939886, rs4939887, rs4939888]0.5500.0
p@chr19:45411878..45411884,- [rs7412]0.520.0160.0
p2@F2 [rs2070852, rs5896]0.510.0160.0
+ linkage disequilibrium:rs2070852:rs4752927 D'=1.0; r2=0.29. p@chr11:46702222..46702264,- [rs4752927]
rs5896:rs4752927 D'=1.0; r2=0.84. p@chr11:46702222..46702264,- [rs4752927]
0.2610.38
p1@APOA5 [rs651821]0.50.0320.0
+ linkage disequilibrium:rs651821:rs11216164 D'=1.0; r2=0.06. p@chr11:116734451..116734464,- [rs11216164]0.0910.79
p8@ALDH1A2 [rs1122208]0.480.0630.01
chr8:19824080..19824096,+ [rs1059507, rs3735964]0.480.0790.01
+ linkage disequilibrium:rs3735964:rs1569209 D'=1.0; r2=0.87. p@chr8:19830089..19830095,+ [rs1569209]0.2910.29
enhancer@chr7:73037168-73037552 [rs55747707]0.480.0790.01
p2@ENST00000519197 [rs28597716]0.480.0950.01
p@chr2:165603312..165603317,- [rs10178921]0.450.240.02
+ linkage disequilibrium:rs10178921:rs355894 D'=1.0; r2=0.22. enhancer@chr2:165635333-165635585 [rs355894]0.1110.76
+ linkage disequilibrium:rs10178921:rs355863 D'=1.0; r2=1.0. p10@COBLL1 [rs355863]0.110.77
p@chr8:116588829..116588841,+ [rs2049867]0.440.350.02
p8@MMP9 [rs2236416]0.430.550.03
p@chr19:11334017..11334033,- [rs4804154, rs4804155]0.430.550.03
+ linkage disequilibrium:rs4804154:rs737337 D'=0.92; r2=0.66. p@chr19:11347228..11347241,- [rs737337]
rs4804155:rs737337 D'=0.92; r2=0.66. p@chr19:11347228..11347241,- [rs737337]
0.3510.17
p@chr19:52327915..52327926,+ [rs3752125]0.410.08
chr11:122526685..122526694,+ [rs7127978]0.3910.09
p@chr7:17287199..17287204,+ [rs6968554]0.3810.1
p@chr15:58576429..58576468,- [rs1711037]0.3810.1
p@chr12:20473724..20473755,+ [rs7134375]0.3810.1
p@chr4:88057279..88057283,+ [rs1408]0.3710.14
p5@INHBE [rs3809114]0.3610.14
p3@LIPC [rs2070895]0.3610.15
chr11:48066327..48066358,+ [rs7934659]0.3510.17
enhancer@chr15:58884938-58885321 [rs11637365]0.3410.18
p@chr19:8468345..8468362,+ [rs2230876]0.3310.2
p@chr2:211540478..211540490,+ [rs1047891]0.3310.2
p@chr16:68114139..68114174,+ [rs7188085]0.3210.23
p@chr6:32412666..32412686,+ [rs7194]0.3210.23
p@chr12:124433988..124434017,- [rs2178663]0.3210.23
+ linkage disequilibrium:rs2178663:rs9863 D'=1.0; r2=0.92. p@chr12:124421545..124421559,- [rs9863]0.110.76
p7@ZDHHC18 [rs12760759]0.310.28
+ linkage disequilibrium:rs12760759:rs17162313 D'=1.0; r2=1.0. enhancer@chr1:27175784-27176273 [rs17162313]0.1910.57
+ linkage disequilibrium:rs12760759:rs1883660 D'=1.0; r2=0.59. enhancer@chr1:27191386-27191927 [rs1883660]0.0610.84
p@chr11:126226533..126226546,- [rs73632737]0.310.28
chr15:63346713..63346752,+ [rs4468558]0.2910.29
+ linkage disequilibrium:rs4468558:rs7174174 D'=0.94; r2=0.83. chr15:63372403..63372411,- [rs7174174]0.1910.57
p14@FADS1 [rs174548, rs174549, rs174550]0.2910.31
p@chr16:56742451..56742454,- [rs4238789]0.2710.36
p4@NISCH [rs4687618]0.2710.36
+ linkage disequilibrium:rs4687618:rs887515 D'=1.0; r2=0.25. p33@NISCH [rs887515]0.110.76
p3@TGOLN2 [rs10460587]0.2610.4
enhancer@chr6:30796195-30796565 [rs1264350]0.2510.4
p@chr19:54775040..54775082,- [rs419304]0.2510.4
p@chr17:76377571..76377602,- [rs4082919]0.2510.42
p@chr16:68299481..68299485,- [rs12596500]0.2410.42
+ linkage disequilibrium:rs12596500:rs12447119 D'=1.0; r2=0.87. p5@SLC7A6 [rs12447119]0.1810.57
+ linkage disequilibrium:rs12596500:rs7184821 D'=1.0; r2=0.5. p2@ESRP2 [rs7184821]0.1710.57
p@chr16:67581701..67581719,- [rs13334205]0.2410.42
chr10:5799591..5799598,+ [rs2275774]0.2410.42
p@chr19:45242420..45242462,+ [rs1531517]0.2410.42
p@chr4:103212519..103212530,- [rs233807]0.2410.43
enhancer@chr1:230289705-230290142 [rs7551742]0.2310.46
+ linkage disequilibrium:rs7551742:rs4846905 D'=0.93; r2=0.83. enhancer@chr1:230279464-230279771 [rs4846905]0.1810.57
p@chr17:37970009..37970013,- [rs9909593]0.2210.46
p@chr4:157683775..157683778,- [rs1425486]0.210.55
p@chr11:45880009..45880015,+ [rs1401417]0.210.57
p@chr10:46076251..46076291,- [rs7086046]0.1910.57
p@chr9:15298766..15298791,+ [rs675849]0.1810.57
p2@CU690121 [rs12225230]0.1810.57
p1@ENST00000438127 [rs3181]0.1810.57
+ linkage disequilibrium:rs3181:rs10892074 D'=1.0; r2=0.17. p@chr11:116980715..116980720,- [rs10892074]0.1410.64
+ linkage disequilibrium:rs3181:rs7930264 D'=1.0; r2=0.89. enhancer@chr11:116870646-116870996 [rs7930264]0.0710.83
enhancer@chr6:34663389-34663600 [rs3800457, rs3800458]0.1710.57
+ linkage disequilibrium:rs3800457:rs11757370 D'=1.0; r2=0.3. enhancer@chr6:34760607-34760986 [rs11757370, rs11755420]
rs3800457:rs11755420 D'=1.0; r2=0.3. enhancer@chr6:34760607-34760986 [rs11757370, rs11755420]
rs3800458:rs11757370 D'=1.0; r2=0.89. enhancer@chr6:34760607-34760986 [rs11757370, rs11755420]
rs3800458:rs11755420 D'=1.0; r2=0.89. enhancer@chr6:34760607-34760986 [rs11757370, rs11755420]
0.1510.62
+ linkage disequilibrium:rs3800457:rs2764205 D'=1.0; r2=0.96. p1@ENST00000408001 [rs2764205]
rs3800458:rs2764205 D'=1.0; r2=0.28. p1@ENST00000408001 [rs2764205]
0.0710.83
p5@BAZ1B [rs1178979]0.1710.57
p@chr8:126447258..126447275,+ [rs2385114]0.1710.57
p@chr1:93627656..93627659,- [rs4847235]0.1710.57
enhancer@chr10:65274637-65275000 [rs10761779]0.1610.59
p2@APOM [rs3117583]0.1610.59
+ linkage disequilibrium:rs3117583:rs3130618 D'=1.0; r2=1.0. p6@GPANK1 [rs3130618]0.1310.68
+ linkage disequilibrium:rs3117583:rs3115663 D'=1.0; r2=1.0. p5@PRRC2A [rs3115663]0.0210.95
p@chr20:33356385..33356390,- [rs2295353]0.1510.62
p@chr11:117075245..117075293,- [rs508487]0.1410.66
p@chr11:46934513..46934519,+ [rs79920646, rs7120113]0.1310.68
p@chr6:139843931..139843972,+ [rs4896469]0.1310.7
p4@TMEM110 [rs11720228]0.1210.72
enhancer@chr15:58712788-58712944 [rs11854624]0.110.76
+ linkage disequilibrium:rs11854624:rs17821310 D'=1.0; r2=0.86. p1@LIPC [rs17821310]0.110.77
p@chr10:65121474..65121480,- [rs12355784]0.0910.78
enhancer@chr12:123387713-123388070 [rs10847980]0.0810.79
p6@PSORS1C1 [rs1265099]0.0810.81
+ linkage disequilibrium:same SNP, different promoter: chr6:31105474..31105493,+ [rs1265099]0.0110.98
enhancer@chr6:127481688-127482073 [rs9491700]0.0610.84
enhancer@chr2:227172292-227172683 [rs2713556]0.0610.84
p7@RBM6 [rs6772095]0.0510.86
enhancer@chr1:39736190-39736575 [rs4660603]0.0510.86
p5@NOL3 [rs2233455]0.0310.93
p@chr17:37405559..37405561,- [rs2061342]0.0310.93
p@chr16:19871741..19871755,- [rs11865578]0.0310.93
p3@PACSIN1 [rs11758326]0.011.0
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Full results table
Layout file (open with Biolayout)