JOB ID = LDL_db138thresh5e-06_complete_BACKCIRC_pj0.1_f5ep

Of 4644 SNPs in input data, 205 were found in FANTOM5 TSS regions (300-TSS-100bp). The input set contained 5.16 SNPs per million bases in TSS regions, compared with 1.47 SNPs per million bases genome-wide. 321 TSS regions were hit, in 92 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.

No significantly enriched cell types in this analysis.

Top promoter[SNPs in top promoter]Corrected
coexpression
score
Bonferroni-corrected
p-value
FDR
p94@APOB [rs1801701]0.7700.0
p@chr17:64210704..64210723,+ [rs1801689]0.7300.0
p3@ABCG5 [rs11887534]0.6600.0
+ linkage disequilibrium:rs11887534:rs13395550 D'=0.25; r2=0.06. enhancer@chr2:44007303-44007575 [rs13395550]0.0610.87
p2@ENST00000518619 [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]
0.2110.46
p2@ASCC2 [rs4823054]0.5700.0
p1@APOA5 [rs651821]0.5500.0
p6@HNF1A-AS1 [rs1169286]0.5400.0
+ linkage disequilibrium:rs1169286:rs2258287 D'=0.68; r2=0.39. p1@C12orf43 [rs2258287]0.1810.55
p@chr19:19616795..19616800,+ [rs1063966]0.5300.0
+ linkage disequilibrium:rs1063966:rs4808967 D'=1.0; r2=1.0. p@chr19:19640454..19640461,+ [rs4808967]0.2410.36
p2@LPIN3 [rs6029636]0.530.0170.0
p@chr16:72075048..72075055,- [rs9932951]0.520.0170.0
+ linkage disequilibrium:rs9932951:rs3213422 D'=0.29; r2=0.08. p1@DHODH [rs34270657, rs3213422]0.430.520.03
p2@NPC1L1 [rs41279633, rs17655652]0.510.0170.0
+ linkage disequilibrium:rs17655652:rs732797 D'=0.92; r2=0.4. p@chr7:44646674..44646689,+ [rs732797]0.1710.57
p@chr1:109727753..109727759,+ [rs12239854]0.490.0510.0
p1@SPC24 [rs892114, rs7251031]0.470.170.01
p1@FRK [rs1999929]0.450.30.02
p3@SLC22A1 [rs12208357]0.430.640.04
p4@HMGCR [rs3761740]0.420.790.05
p12@TRIB1 [rs17405319]0.420.810.05
p1@FEN1 [rs174538, rs412334]0.410.90.05
+ linkage disequilibrium:rs174538:rs412334 D'=1.0; r2=0.07. p4@C11orf10 [rs412334]
same SNP, different promoter: p4@C11orf10 [rs412334]
0.1210.72
p5@ABCA1 [rs1800978]0.3910.07
p3@TIRAP [rs10893493]0.3710.1
+ linkage disequilibrium:rs10893493:rs638433 D'=0.96; r2=0.92. enhancer@chr11:126180283-126180636 [rs638433]0.1910.53
p@chr1:63112277..63112278,+ [rs1168085]0.3710.1
p@chr2:121310959..121310964,- [rs940688]0.3610.11
p7@PCSK9 [rs11591147, rs11583680]0.3510.12
p3@HAVCR1 [rs67960962]0.3510.12
+ linkage disequilibrium:rs67960962:rs6882076 D'=0.83; r2=0.31. p1@TIMD4 [rs6882076]0.0710.87
p@chr9:136154265..136154271,- [rs579459, rs649129]0.3410.14
chr19:19488822..19488846,+ [rs12973258]0.3310.16
chr6:160770176..160770186,- [rs539298]0.3310.16
p4@TAP2 [rs241448, rs241447, rs241452]0.3310.17
p@chr19:45411878..45411884,- [rs7412]0.3110.2
p3@C6orf10 [rs6913309]0.3110.21
+ linkage disequilibrium:rs6913309:rs13218331 D'=0.87; r2=0.44. p@chr6:32411190..32411212,- [rs13218331]0.2610.31
p@chr8:145010972..145010996,- [rs6993938]0.310.21
p@chr19:45242420..45242462,+ [rs1531517]0.310.21
+ linkage disequilibrium:rs1531517:rs10422182 D'=0.62; r2=0.22. p@chr19:45159154..45159158,+ [rs10422182]0.0910.82
chr19:11031515..11031547,+ [rs2288842]0.2910.23
+ linkage disequilibrium:rs2288842:rs11085749 D'=1.0; r2=0.61. p@chr19:10961151..10961183,+ [rs11085749]0.1710.57
p4@SH2B3 [rs739496]0.2910.23
p@chr2:136594382..136594389,+ [rs2236783]0.2910.23
p1@NAT2 [rs4646246]0.2910.24
enhancer@chr20:34127589-34128004 [rs2104417]0.2710.31
p5@RBM12 [rs6121015]0.2610.31
p31@CORO1C [rs3741782]0.2610.31
p23@USP1 [rs646179]0.2510.36
p4@GSTM4 [rs1010167]0.2310.42
p16@HLX [rs17597773]0.2310.42
p@chr6:32658073..32658091,- [rs9469220]0.2210.44
p12@PLCG1 [rs6124323]0.2110.48
p@chr1:25756820..25756837,+ [rs9438904]0.210.49
p@chr6:31239406..31239455,+ [rs9264664]0.210.51
p1@POC5 [rs2291630]0.1910.53
+ linkage disequilibrium:rs2291630:rs2047059 D'=1.0; r2=0.64. p2@POC5 [rs2047059]0.1410.69
+ linkage disequilibrium:rs2291630:rs7715806 D'=0.95; r2=0.39. enhancer@chr5:75034241-75034569 [rs7715806]0.110.76
+ linkage disequilibrium:rs2291630:rs34358 D'=1.0; r2=0.47. p@chr5:74965139..74965165,+ [rs34358]0.0810.82
p1@SLC44A4 [rs605203]0.1910.53
chr20:39634184..39634189,- [rs1000410]0.1710.57
enhancer@chr16:56985400-56985562 [rs72786786, rs12448528]0.1710.57
p@chr1:63266602..63266609,- [rs11208033]0.1710.57
chr19:10742301..10742328,+ [rs2288904, rs1560711]0.1510.63
p@chr12:112212004..112212016,+ [rs2238151]0.1510.64
p@chr2:216286925..216286942,- [rs1250248]0.1310.7
enhancer@chr14:94813306-94813452 [rs926144]0.1310.7
p4@FUT1 [rs838136]0.1310.7
p3@SPTY2D1 [rs7943121]0.1210.7
enhancer@chr5:74805918-74806308 [rs5744533]0.1110.76
p@chr10:113928643..113928689,- [rs2803616]0.1110.76
p1@ENST00000364447 [rs1003116]0.110.78
enhancer@chr19:46018095-46018753 [rs7255743]0.0810.82
enhancer@chr2:136816831-136817220 [rs749873]0.0810.85
p@chr3:12704990..12705013,- [rs904453]0.0710.85
p@chr11:117075245..117075293,- [rs508487]0.0610.87
enhancer@chr1:109754796-109754995 [rs187413240]0.0610.87
enhancer@chr11:61713558-61713889 [rs1534842]0.0610.87
p@chr6:16131425..16131449,+ [rs2235215, rs2066905]0.0610.87
enhancer@chr8:59311673-59312115 [rs1030431]0.0510.88
p@chr2:135893438..135893485,+ [rs10445686]0.0410.92
enhancer@chr6:34663389-34663600 [rs3800457]0.0410.92
enhancer@chr1:92668364-92668570 [rs3131816]0.0310.92
p3@C17orf57 [rs2271803]0.0310.92
p@chr5:74964235..74964256,+ [rs7715739, rs369034591]0.0210.96
p1@ATXN2 [rs695871]0.0210.96
p@chr6:32078154..32078167,- [rs3807039]0.0210.96
enhancer@chr1:25802039-25802147 [rs66844552]0.0110.96
p@chr6:31512638..31512648,- [rs2071593]0.011.0