JOB ID = uc_db138thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 2162 SNPs in input data, 146 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 3.76 SNPs per million bases in TSS regions, compared with 0.68 SNPs per million bases genome-wide. 234 TSS regions were hit, in 83 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_pool19.7e-070
liver_adult_pool15e-060
macLPS_04hr0.000110
colon_adult_pool10.000190
appendix_adult0.000260
rectum_fetal0.000530
duodenum_fetal_donor1_tech3.3e-050.0073
macLPS_05hr9.8e-050.0073
small_intestine_fetal0.00750.012
macLPS_22hr0.0260.012
macLPS_12hr0.0130.015
spleen_adult_pool10.0410.015
macLPS_18hr0.0190.018
colon_fetal0.0120.033
macLPS_10hr0.0060.035
macLPS_03hr30min0.00220.036
macLPS_24hr0.0350.036
macLPS_20hr0.0360.036
Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p1@TRIM40 [rs9261467]0.6700.0
+ linkage disequilibrium:rs9261467:rs9295829 D'=0.84; r2=0.6. p3@ZNRD1-AS1 [rs9295829]0.3310.05
+ linkage disequilibrium:rs9261467:rs9295829 D'=0.84; r2=0.6. p2@ZNRD1 [rs9295829]0.1610.45
p4@RNF186 [rs12064796]0.6100.0
p2@HLA-DQA1 [rs9272426]0.600.0
p11@C1orf106 [rs7554511]0.5600.0
+ linkage disequilibrium:same SNP, different promoter: p@chr1:200877847..200877851,+ [rs7554511]0.1910.37
+ linkage disequilibrium:rs7554511:rs296533 D'=0.73; r2=0.4. enhancer@chr1:200865457-200866265 [rs296533]0.0810.73
p1@LOC100133445, p1@LOC115110 [rs1886730]0.5400.0
p3@HLA-DQA1 [rs3135391]0.5100.0
+ linkage disequilibrium:rs3135391:rs2050188 D'=1.0; r2=0.47. p2@C6orf10 [rs2050188]0.2810.15
p@chr20:62366043..62366057,+ [rs2427533]0.4800.0
p@chr11:6461452..6461464,- [rs10839564]0.4600.0
p2@LSP1 [rs907611]0.4500.0
p2@FAM55A [rs661946]0.4400.0
p3@X07061, p3@X07062 [rs1058026]0.40.120.01
p2@NKX2-3 [rs10883371, rs10883373]0.40.120.01
p@chr1:206943938..206943954,- [rs3024493]0.390.120.01
p27@CFB [rs1048709]0.370.270.02
p13@TMBIM1 [rs2382817]0.360.390.03
p@chr17:38029166..38029196,+ [rs12936231]0.360.410.03
p5@CCNY [rs12242110]0.360.430.03
p4@PMPCA [rs3812584]0.360.590.03
+ linkage disequilibrium:same SNP, different promoter: p3@PMPCA [rs3812584]0.2910.13
enhancer@chr1:151792678-151793001 [rs949969]0.340.840.04
p7@CREM [rs4934730]0.340.880.04
p4@CXCR2 [rs4674258]0.3310.05
p28@TNIP1 [rs2233287]0.3110.09
p4@MZB1 [rs9327847]0.310.11
p@chr1:8022209..8022235,- [rs3766606]0.310.11
p@chr6:31464084..31464111,- [rs6916394]0.2910.12
+ linkage disequilibrium:rs6916394:rs3828912 D'=1.0; r2=1.0. p@chr6:31465753..31465756,- [rs3828912, rs3828914]
rs6916394:rs3828914 D'=1.0; r2=1.0. p@chr6:31465753..31465756,- [rs3828912, rs3828914]
0.0410.89
p@chr5:498417..498421,- [rs12521198]0.2910.12
enhancer@chr14:98513457-98513851 [rs8008845]0.2710.16
enhancer@chr2:61095090-61095322 [rs842639]0.2710.17
p1@SLC26A3 [rs2301988, rs2301989]0.2610.19
p15@GAL3ST1 [rs7286285]0.2510.21
enhancer@chr18:4003748-4003994 [rs16945853]0.2510.21
enhancer@chr3:49389809-49389972 [rs17080528]0.2310.27
+ linkage disequilibrium:rs17080528:rs11716445 D'=1.0; r2=0.3. p@chr3:49405916..49405955,- [rs11716445]0.0510.83
enhancer@chr5:601191-601577 [rs3749615]0.2310.27
+ linkage disequilibrium:rs3749615:rs7434 D'=1.0; r2=1.0. p@chr5:660645..660655,- [rs7434]0.1410.5
enhancer@chr2:61204524-61204872 [rs7608910]0.2310.27
p@chr6:32186154..32186158,- [rs436388]0.2310.27
+ linkage disequilibrium:rs436388:rs176095 D'=1.0; r2=0.21. p@chr6:32158228..32158249,+ [rs176095]0.1910.37
+ linkage disequilibrium:rs436388:rs3134947 D'=0.92; r2=0.18. p2@AGPAT1 [rs3134947]0.0310.91
p1@GNA12 [rs1636249]0.2310.27
enhancer@chr5:40410103-40410947 [rs6451493, rs11742570]0.2110.32
p@chr3:49139102..49139119,- [rs35673421]0.2110.32
chr2:28203328..28203338,+ [rs898031]0.2110.32
p1@ENST00000448198, p1@ENST00000455328 [rs3916765]0.2110.32
p@chr8:135520294..135520308,- [rs16905158]0.2110.32
enhancer@chr6:42081758-42081907 [rs9462770]0.210.33
p1@RBM5 [rs2247510]0.1910.37
p11@PNMT [rs876493]0.1910.37
p2@TNFRSF6B [rs2297441]0.1910.37
enhancer@chr13:37723502-37723846 [rs17054986]0.1910.37
p@chr3:49591052..49591057,+ [rs3811697]0.1810.39
p@chr6:29635769..29635797,+ [rs1318631]0.1810.4
p9@MMP23B [rs28456011]0.1610.45
chr3:49941317..49941322,- [rs2280406]0.1610.45
+ linkage disequilibrium:rs2280406:rs6772095 D'=1.0; r2=0.87. p7@RBM6 [rs6772095]0.110.69
enhancer@chr21:40466283-40466718 [rs2836882]0.1510.47
p@chr4:148535454..148535476,- [rs931779]0.1510.49
p@chr1:110364218..110364229,+ [rs2938616]0.1310.56
p@chr5:149627361..149627384,- [rs7711562]0.1210.61
p@chr12:7032510..7032525,+ [rs10849541]0.1110.63
enhancer@chr1:36715455-36715834 [rs11263868]0.110.68
enhancer@chr5:158826036-158826401 [rs918519]0.110.68
p4@PRKAR1B [rs4074132]0.110.68
p1@ENST00000431069 [rs3780373]0.0910.73
enhancer@chr6:30716597-30717062 [rs12210092]0.0810.73
enhancer@chr3:138565329-138565569 [rs11716652]0.0810.73
chr2:127816629..127816649,+ [rs17014835]0.0710.79
p1@MLH3 [rs175083]0.0610.79
p12@LAMB1 [rs2158836]0.0610.79
enhancer@chr17:25691108-25691369 [rs322207]0.0610.82
enhancer@chr7:22711367-22711465 [rs17147141]0.0410.89
p1@ZFP90 [rs1170445, rs1170444]0.0310.9
enhancer@chr12:8147722-8148111 [rs10161016]0.0310.9
p1@SLC38A3 [rs1858828]0.0110.97
p@chr13:77463947..77463954,- [rs17066875]0.011.0
p2@RPL22 [rs4908865]0.011.0