JOB ID = cd-meta-remapped_first_db138thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 1924 SNPs in input data, 133 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 3.49 SNPs per million bases in TSS regions, compared with 0.61 SNPs per million bases genome-wide. 217 TSS regions were hit, in 70 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
CD14pos_Monocytes1.8e-170
Peripheral_Blood_Mononuclear_Cells2.8e-140
CD14_monocytes_treated_with_Trehalose4.7e-140
CD14_monocytes_treated_with_BCG7.4e-140
CD14_monocytes_treated_with_Candida8.2e-140
CD14_monocytes_treated_with_Group_A_streptococci9.5e-130
CD14_monocytes_treated_with_Salmonella9.7e-130
Basophils1.7e-120
CD14_monocytes_treated_with_IFN_Nhexane2e-090
CD14pos_CD16pos_Monocytes2e-090
CD4_CD25CD45RA_memory_conventional_T_cells1.5e-080
Natural_Killer_Cells7.3e-080
CD4_T_Cells7.4e-070
CD14neg_CD16pos_Monocytes3.7e-050
CD14_monocytes_treated_with_lipopolysaccharide8e-120.0039
CD8_T_Cells_pluriselect5.6e-050.0073
CD34_Progenitors1.4e-060.0087
CD19_B_Cells1.1e-050.0087
CD14_monocytes_mock_treated3.4e-050.0087
Dendritic_Cells_plasmacytoid0.000690.0087
CD14_monocytes_treated_with_Bglucan6.6e-080.011
CD14_monocytes_treated_with_Cryptococcus1e-060.015
CD4_CD25_CD45RA_memory_regulatory_T_cells_expanded0.00850.015
CD8_T_Cells3.2e-050.019
CD14pos_CD16neg_Monocytes0.000720.021
CD4_CD25_CD45RA_memory_regulatory_T_cells0.00170.039
Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p@chr5:131820136..131820148,- [rs2070727]0.6800.0
enhancer@chr2:61112067-61112568 [rs6545835]0.6200.0
p@chr1:67896878..67896883,+ [rs3762313, rs3762314]0.6100.0
enhancer@chr5:40486540-40486993 [rs7720838]0.5700.0
p4@TAP2 [rs241448, rs241447, rs241452, rs17034, rs241451, rs241449]0.5500.0
enhancer@chr22:30591785-30593544 [rs713875]0.5200.0
p@chr6:31240851..31240879,- [rs7759127]0.5200.0
p@chr10:35484899..35484906,- [rs1057108]0.4900.0
p@chr17:32635480..32635483,- [rs16969454]0.4800.0
p@chr17:37970009..37970013,- [rs9909593]0.4600.0
enhancer@chr15:67468171-67468380 [rs17294280]0.4400.0
enhancer@chr14:88472465-88473193 [rs8005161]0.430.0230.0
enhancer@chr10:82253401-82253904 [rs7900536]0.410.0690.0
p1@DAP3 [rs1058207]0.410.0690.0
p@chr6:32405128..32405175,- [rs3135395]0.410.0920.01
p1@RPL37 [rs10065570]0.380.140.01
enhancer@chr21:45627966-45628150 [rs2838522]0.380.160.01
p@chr14:69261497..69261515,+ [rs2236262]0.340.320.02
p@chr2:43521231..43521252,+ [rs1322]0.340.480.03
p8@LNPEP [rs2351010]0.320.620.03
p1@C6orf48 [rs9368699]0.320.640.03
enhancer@chr1:206939730-206940044 [rs3024505]0.320.640.03
p3@CISD1 [rs2790189]0.310.940.04
p@chr2:102931037..102931044,+ [rs12712135]0.2910.08
p@chr20:62366061..62366072,+ [rs2427533]0.2810.09
p@chr10:64397428..64397447,- [rs16917546, rs10761652]0.2710.09
p4@CD244 [rs12036607, rs7410867, rs12036670]0.2610.12
p@chr1:7886661..7886674,+ [rs697693]0.2310.2
p21@SEC16A [rs3812591]0.2310.2
+ linkage disequilibrium:rs3812591:rs3812584 D'=1.0; r2=0.38. p3@PMPCA [rs3812584]0.1710.36
p@chr10:81053715..81053725,+ [rs1250560, rs1250559]0.2310.22
enhancer@chr2:43745392-43745589 [rs10189235]0.2210.23
p1@RNU86 [rs12484030]0.2210.23
p1@AK131570 [rs9252]0.2210.23
p3@SCAMP3 [rs1046188]0.2110.25
p@chr3:49360037..49360041,- [rs9873994]0.1910.29
p6@HIPK1 [rs3811019]0.1910.29
enhancer@chr1:155951073-155951535 [rs1889532]0.1910.29
enhancer@chr6:159514738-159514976 [rs654690]0.1910.31
p@chr6:31543810..31543821,- [rs3093661]0.1810.33
p3@TNXB [rs8283]0.1810.34
enhancer@chr6:167411692-167411848 [rs239935]0.1810.34
p1@ENST00000431069 [rs3780373]0.1710.35
enhancer@chr1:155433776-155433971 [rs12724079]0.1610.38
p7@RBM6 [rs6772095]0.1610.41
p2@uc001flf.2 [rs2048431]0.1510.44
p@chr6:32186154..32186158,- [rs438475]0.1410.46
p@chr1:200877847..200877851,+ [rs7554511]0.1310.54
enhancer@chr6:20811412-20811642 [rs9465900]0.1210.55
p2@ATP2A1 [rs3888190]0.1210.55
p14@FADS1 [rs174548]0.1210.55
p1@RBM5 [rs2247510]0.1210.55
p3@GON4L [rs3820594]0.110.62
chr16:50668341..50668342,+ [rs12913]0.0910.62
enhancer@chr5:158848054-158848257 [rs4921496]0.0910.62
p4@SLC9A4 [rs4851011]0.0910.63
p1@ZNF300 [rs7724036]0.0910.63
p@chr5:158705320..158705331,+ [rs12520035]0.0910.64
p13@DGKD [rs838718]0.0810.65
p2@TNFRSF6B [rs2297441]0.0810.68
+ linkage disequilibrium:rs2297441:rs11696871 D'=0.96; r2=0.61. chr20:62387380..62387381,- [rs11696871]0.0110.97
p2@NKX2-3 [rs10883371]0.0610.74
p5@LRRK2 [rs1388597]0.0510.8
p1@SCARNA5 [rs3792109]0.0410.86
p@chr3:49570849..49570853,+ [rs1050088]0.0310.91
+ linkage disequilibrium:rs1050088:rs3811697 D'=1.0; r2=0.32. p@chr3:49591052..49591057,+ [rs3811697]0.0210.92
p9@EBF1 [rs7442701]0.0310.91
enhancer@chr16:50554457-50554868 [rs12930566]0.0210.92
p1@GTF2H4 [rs2074510]0.0210.92
p@chr6:134637878..134637882,- [rs6923743]0.011.0