White Blood - Prostate
sheng Qian
2022-10-18
Last updated: 2023-01-26
Checks: 5 2
Knit directory: cTWAS_analysis/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20211220) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.
| absolute | relative |
|---|---|
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/ | data |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config_b38.R | code/ctwas_config_b38.R |
| /project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/mqtl/Prostate.db | data/mqtl/Prostate.db |
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 6bad70c. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .ipynb_checkpoints/
Untracked files:
Untracked: Proposal plots.R
Untracked: RGS14.pdf
Untracked: RNF186.pdf
Untracked: SCZ_annotation.xlsx
Untracked: SLC8B1.pdf
Untracked: analysis/.ipynb_checkpoints/
Untracked: analysis/Single_QTL_Analysis.Rmd
Untracked: analysis/WhiteBlood_Prostate_M.Rmd
Untracked: analysis/WhiteBlood_WholeBlood_M.Rmd
Untracked: cache/
Untracked: code/.ipynb_checkpoints/
Untracked: code/RedBlood_M_out/
Untracked: code/White_Blood_M_out/
Untracked: code/run_RedBlood_analysis_M.sbatch
Untracked: code/run_RedBlood_analysis_M.sh
Untracked: code/run_RedBlood_ctwas_rss_LDR_M.R
Untracked: data/.ipynb_checkpoints/
Untracked: data/FUMA_output/
Untracked: data/GO_Terms/
Untracked: data/GTEx_Analysis_v8_eQTL.tar
Untracked: data/IBD_ME/
Untracked: data/LDL/
Untracked: data/LDL_E_S/
Untracked: data/LDL_M/
Untracked: data/LDL_S/
Untracked: data/LDL_multi/
Untracked: data/PGC3_SCZ_wave3_public.v2.tsv
Untracked: data/RedBlood_M/
Untracked: data/SCZ/
Untracked: data/SCZ_2014_EUR/
Untracked: data/SCZ_2014_EUR_ME/
Untracked: data/SCZ_2018/
Untracked: data/SCZ_2018_ME/
Untracked: data/SCZ_2018_S/
Untracked: data/SCZ_2020/
Untracked: data/SCZ_S/
Untracked: data/Supplementary Table 15 - MAGMA.xlsx
Untracked: data/Supplementary Table 20 - Prioritised Genes.xlsx
Untracked: data/UKBB/
Untracked: data/UKBB_SNPs_Info.text
Untracked: data/White_Blood_M/
Untracked: data/eqtl/
Untracked: data/gene_OMIM.txt
Untracked: data/gene_pip_0.8.txt
Untracked: data/gwas_sumstats/
Untracked: data/magma.genes.out
Untracked: data/mashr_Heart_Atrial_Appendage.db
Untracked: data/mashr_sqtl/
Untracked: data/mqtl/
Untracked: data/multigroup/
Untracked: data/notes.txt
Untracked: data/scz_2018.RDS
Untracked: data/summary_known_genes_annotations.xlsx
Untracked: temp_LDR/
Untracked: top_genes_32.txt
Untracked: top_genes_37.txt
Untracked: top_genes_43.txt
Untracked: top_genes_54.txt
Untracked: top_genes_81.txt
Untracked: z_snp_pos_SCZ.RData
Untracked: z_snp_pos_SCZ_2014_EUR.RData
Untracked: z_snp_pos_SCZ_2018.RData
Untracked: z_snp_pos_SCZ_2020.RData
Unstaged changes:
Deleted: analysis/BMI_S_results.Rmd
Modified: analysis/LDL_Blood_M.Rmd
Modified: analysis/index.Rmd
Modified: code/LDL_M_out/LDL_BreastMammary.err
Modified: code/LDL_M_out/LDL_BreastMammary.out
Modified: code/LDL_M_out/LDL_ColonTransverse.err
Modified: code/LDL_M_out/LDL_ColonTransverse.out
Modified: code/LDL_M_out/LDL_Lung.err
Modified: code/LDL_M_out/LDL_Lung.out
Modified: code/LDL_M_out/LDL_Ovary.err
Modified: code/LDL_M_out/LDL_Ovary.out
Deleted: code/run_IBD_ctwas_rss_LDR_ME.R
Modified: code/run_LDL_analysis_M.sh
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.
Weight QC
[1] 48748[1] 43661
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
4104 3452 2299 1938 2229 2922 2432 1993 1233 2189 2583 2100 1147 1395 1414 2130
17 18 19 20 21 22
2453 756 1841 1210 708 1133 [1] 1Load ctwas results
Check convergence of parameters
#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior) SNP gene
0.0002067 0.0076251 #estimated group prior variance
estimated_group_prior_var <- estimated_group_prior_var_all[,ncol(group_prior_var_rec)]
print(estimated_group_prior_var) SNP gene
17.08 25.87 #estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)[1] 36.88#report sample size
print(sample_size)[1] 350470#report group size
print(group_size) SNP gene
8696600 43661 #estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve) SNP gene
0.08761 0.02458 #total PVE
sum(estimated_group_pve)[1] 0.1122#attributable PVE
estimated_group_pve/sum(estimated_group_pve) SNP gene
0.7809 0.2191 Genes with highest PIPs
#distribution of PIPs
hist(ctwas_gene_res$susie_pip, xlim=c(0,1), main="Distribution of Gene PIPs")
#genes with PIP>0.8 or 20 highest PIPs
head(ctwas_gene_res[order(-ctwas_gene_res$susie_pip),report_cols], max(sum(ctwas_gene_res$susie_pip>0.8), 20)) genename region_tag id susie_pip mu2
21130 GCNT2 6_9 cg11118520 1.0000 7149.66
44652 ZBTB22 6_28 cg25191172 0.9909 177.59
10634 <NA> 6_24 cg05505711 0.9828 164.88
8001 <NA> 1_41 cg04111102 0.9647 174.01
30125 RP11-14C10.4 15_50 cg16103421 0.9630 35.05
21908 DPH1 17_2 cg11577151 0.9562 25.06
29469 AC034220.3;SLC22A5 5_79 cg15738769 0.9547 130.81
6808 <NA> 2_140 cg03472961 0.9519 34.00
11720 AC006126.4;MARK4 19_31 cg06112816 0.9502 270.67
36599 KDELC2 11_63 cg20058057 0.9450 29.64
17132 LYN 8_43 cg08894788 0.9424 50.17
44405 VLDLR;VLDLR-AS1 9_3 cg25032030 0.9251 46.75
39536 KDM4B 19_5 cg21973527 0.9241 30.75
46332 <NA> 18_11 cg26234723 0.9149 22.92
21856 PTPRJ 11_29 cg11545521 0.9130 69.71
16593 <NA> 11_74 cg08637269 0.8979 67.63
26543 <NA> 10_83 cg14138475 0.8942 35.35
45859 TTC39C 18_12 cg25952192 0.8834 32.18
33165 PAX8;PAX8-AS1;RP11-65I12.1 2_67 cg17774569 0.8816 36.18
34842 SPTLC2 14_36 cg18872420 0.8735 30.35
30365 ATXN7;THOC7 3_43 cg16258503 0.8589 24.00
35811 GPRIN3 4_60 cg19537443 0.8527 26.82
16511 SMG9 19_30 cg08581076 0.8489 34.87
44630 VAMP5 2_54 cg25178838 0.8165 37.39
34253 CD82 11_27 cg18496383 0.8147 24.35
38057 PADI1 1_12 cg21010178 0.8142 23.65
44782 <NA> 21_18 cg25269340 0.8139 60.02
32216 EHD4 15_15 cg17244218 0.8125 108.37
12790 GPR116 6_35 cg06673956 0.8107 33.74
PVE z num_eqtl
21130 2.040e-02 -3.928 1
44652 5.021e-04 9.566 1
10634 4.624e-04 -1.928 1
8001 4.790e-04 -16.175 1
30125 9.631e-05 5.765 1
21908 6.838e-05 -4.388 1
29469 3.563e-04 13.657 1
6808 9.236e-05 -7.559 1
11720 7.339e-04 14.933 1
36599 7.991e-05 -6.197 1
17132 1.349e-04 7.116 1
44405 1.234e-04 6.429 1
39536 8.108e-05 -5.487 1
46332 5.983e-05 -4.062 1
21856 1.816e-04 -9.930 1
16593 1.733e-04 8.437 1
26543 9.020e-05 -5.918 1
45859 8.112e-05 4.551 1
33165 9.101e-05 6.672 1
34842 7.563e-05 2.576 1
30365 5.882e-05 -4.033 1
35811 6.525e-05 -4.645 1
16511 8.447e-05 4.701 1
44630 8.712e-05 -5.035 1
34253 5.661e-05 4.524 1
38057 5.495e-05 -4.362 1
44782 1.394e-04 -7.733 1
32216 2.512e-04 -12.597 1
12790 7.805e-05 5.585 1Genes with largest effect sizes
#plot PIP vs effect size
plot(ctwas_gene_res$susie_pip, ctwas_gene_res$mu2, xlab="PIP", ylab="mu^2", main="Gene PIPs vs Effect Size")
#genes with 20 largest effect sizes
head(ctwas_gene_res[order(-ctwas_gene_res$mu2),report_cols],20) genename region_tag id susie_pip mu2 PVE z
41552 LSS 21_24 cg23289605 0 15995 0.0000 -4.8444
18868 LSS 21_24 cg09831081 0 13275 0.0000 -5.2615
22244 PCNT 21_24 cg11764399 0 9266 0.0000 4.5844
21130 GCNT2 6_9 cg11118520 1 7150 0.0204 -3.9282
26726 PCNT 21_24 cg14233374 0 6896 0.0000 4.9575
20725 PCNT 21_24 cg10878966 0 6314 0.0000 5.5785
5838 PCNT 21_24 cg02959939 0 6302 0.0000 5.5187
32742 HCP5;MICA 6_25 cg17529716 0 5615 0.0000 11.2491
18123 YBEY 21_24 cg09417038 0 5411 0.0000 -0.9051
23528 <NA> 21_24 cg12516959 0 5258 0.0000 -0.8848
1720 <NA> 21_24 cg00815214 0 5258 0.0000 -0.8848
43386 <NA> 6_25 cg24439364 0 4395 0.0000 10.8185
1282 <NA> 21_24 cg00612595 0 3936 0.0000 -0.9678
48178 HCP5;LINC01149 6_25 cg27326026 0 3767 0.0000 12.0717
32640 HCP5;MICA 6_25 cg17476405 0 3416 0.0000 14.4636
33606 LSS;MCM3AP-AS1 21_24 cg18069493 0 3406 0.0000 4.0912
14245 HCP5;MICA 6_25 cg07376033 0 3331 0.0000 11.7810
22003 PCNT 21_24 cg11628223 0 2979 0.0000 -1.7442
41 RNU6-1133P 6_25 cg00020172 0 2921 0.0000 -28.4773
47373 HCP5;MICA;Y_RNA 6_25 cg26846810 0 2850 0.0000 6.9007
num_eqtl
41552 1
18868 1
22244 1
21130 1
26726 1
20725 1
5838 1
32742 1
18123 1
23528 1
1720 1
43386 1
1282 1
48178 1
32640 1
33606 1
14245 1
22003 1
41 1
47373 1Genes with highest PVE
#genes with 20 highest pve
head(ctwas_gene_res[order(-ctwas_gene_res$PVE),report_cols],20) genename region_tag id susie_pip mu2 PVE
21130 GCNT2 6_9 cg11118520 1.0000 7149.66 0.0204002
14343 PSMD3 17_23 cg07427276 0.7984 622.59 0.0014183
11720 AC006126.4;MARK4 19_31 cg06112816 0.9502 270.67 0.0007339
24271 XXbac-BPG308K3.6 6_22 cg12914966 0.7554 321.11 0.0006921
44652 ZBTB22 6_28 cg25191172 0.9909 177.59 0.0005021
13981 CHD7 8_46 cg07228241 0.7942 212.30 0.0004811
8001 <NA> 1_41 cg04111102 0.9647 174.01 0.0004790
10634 <NA> 6_24 cg05505711 0.9828 164.88 0.0004624
29469 AC034220.3;SLC22A5 5_79 cg15738769 0.9547 130.81 0.0003563
9793 ZPBP2 17_23 cg05057505 0.6335 189.00 0.0003416
42089 MSH5;MSH5-SAPCD1 6_26 cg23634079 0.3764 309.02 0.0003319
30848 C2;ZBTB12 6_26 cg16505946 0.3764 309.02 0.0003319
46716 <NA> 17_23 cg26458775 0.1714 619.42 0.0003030
29677 PREX1 20_30 cg15849237 0.6005 162.21 0.0002780
32216 EHD4 15_15 cg17244218 0.8125 108.37 0.0002512
21856 PTPRJ 11_29 cg11545521 0.9130 69.71 0.0001816
16593 <NA> 11_74 cg08637269 0.8979 67.63 0.0001733
38255 PREX1 20_30 cg21145944 0.3599 163.39 0.0001678
47128 REST 4_41 cg26694713 0.7433 78.03 0.0001655
4819 PAK2;U4 3_121 cg02455773 0.5334 106.62 0.0001623
z num_eqtl
21130 -3.928 1
14343 -37.218 1
11720 14.933 1
24271 19.798 1
44652 9.566 1
13981 2.826 1
8001 -16.175 1
10634 -1.928 1
29469 13.657 1
9793 23.719 1
42089 26.924 1
30848 -26.924 1
46716 -37.059 1
29677 -2.590 1
32216 -12.597 1
21856 -9.930 1
16593 8.437 1
38255 2.394 1
47128 -9.062 1
4819 9.125 1Genes with largest z scores
#genes with 20 largest z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag id susie_pip mu2
14343 PSMD3 17_23 cg07427276 7.984e-01 622.6
46716 <NA> 17_23 cg26458775 1.714e-01 619.4
32508 MED24;THRA 17_23 cg17401724 4.598e-10 406.2
31946 HLA-C 6_25 cg17096289 0.000e+00 846.3
41 RNU6-1133P 6_25 cg00020172 0.000e+00 2920.5
6981 MED24;MIR6884 17_23 cg03568305 6.590e-10 350.2
6598 MED24;MIR6884 17_23 cg03367679 6.590e-10 350.2
9762 TNXB 6_26 cg05045332 1.110e-16 417.9
11743 <NA> 17_23 cg06123174 8.195e-08 294.0
9784 APOM;BAG6 6_26 cg05053818 0.000e+00 445.5
46204 GSDMA 17_23 cg26162295 6.643e-11 262.9
26619 SKIV2L 6_26 cg14178705 0.000e+00 420.5
44201 GSDMA 17_23 cg24910161 5.043e-11 237.5
18438 HLA-B;HLA-C;XXbac-BPG248L24.12 6_25 cg09588770 0.000e+00 858.0
42089 MSH5;MSH5-SAPCD1 6_26 cg23634079 3.764e-01 309.0
30848 C2;ZBTB12 6_26 cg16505946 3.764e-01 309.0
13216 BTNL2 6_26 cg06871764 0.000e+00 397.3
44275 <NA> 6_26 cg24965496 0.000e+00 446.6
31319 HLA-DRA 6_26 cg16753237 0.000e+00 300.2
39715 <NA> 6_25 cg22110654 6.433e-10 796.6
PVE z num_eqtl
14343 1.418e-03 -37.22 1
46716 3.030e-04 -37.06 1
32508 5.330e-13 -30.92 1
31946 0.000e+00 28.80 1
41 0.000e+00 -28.48 1
6981 6.584e-13 28.44 1
6598 6.584e-13 28.44 1
9762 1.324e-19 -28.30 1
11743 6.875e-11 28.01 1
9784 0.000e+00 27.89 1
46204 4.983e-14 -27.87 1
26619 0.000e+00 -27.59 1
44201 3.418e-14 -27.47 1
18438 0.000e+00 27.12 1
42089 3.319e-04 26.92 1
30848 3.319e-04 -26.92 1
13216 0.000e+00 26.79 1
44275 0.000e+00 26.43 1
31319 0.000e+00 26.11 1
39715 1.462e-12 -25.85 1Comparing z scores and PIPs
#set nominal signifiance threshold for z scores
alpha <- 0.05
#bonferroni adjusted threshold for z scores
sig_thresh <- qnorm(1-(alpha/nrow(ctwas_gene_res)/2), lower=T)
#Q-Q plot for z scores
obs_z <- ctwas_gene_res$z[order(ctwas_gene_res$z)]
exp_z <- qnorm((1:nrow(ctwas_gene_res))/nrow(ctwas_gene_res))
plot(exp_z, obs_z, xlab="Expected z", ylab="Observed z", main="Gene z score Q-Q plot")
abline(a=0,b=1)
#plot z score vs PIP
plot(abs(ctwas_gene_res$z), ctwas_gene_res$susie_pip, xlab="abs(z)", ylab="PIP")
abline(v=sig_thresh, col="red", lty=2)
#number of significant z scores
sum(abs(ctwas_gene_res$z) > sig_thresh)[1] 1431#proportion of significant z scores
mean(abs(ctwas_gene_res$z) > sig_thresh)[1] 0.03278#genes with most significant z scores
head(ctwas_gene_res[order(-abs(ctwas_gene_res$z)),report_cols],20) genename region_tag id susie_pip mu2
14343 PSMD3 17_23 cg07427276 7.984e-01 622.6
46716 <NA> 17_23 cg26458775 1.714e-01 619.4
32508 MED24;THRA 17_23 cg17401724 4.598e-10 406.2
31946 HLA-C 6_25 cg17096289 0.000e+00 846.3
41 RNU6-1133P 6_25 cg00020172 0.000e+00 2920.5
6981 MED24;MIR6884 17_23 cg03568305 6.590e-10 350.2
6598 MED24;MIR6884 17_23 cg03367679 6.590e-10 350.2
9762 TNXB 6_26 cg05045332 1.110e-16 417.9
11743 <NA> 17_23 cg06123174 8.195e-08 294.0
9784 APOM;BAG6 6_26 cg05053818 0.000e+00 445.5
46204 GSDMA 17_23 cg26162295 6.643e-11 262.9
26619 SKIV2L 6_26 cg14178705 0.000e+00 420.5
44201 GSDMA 17_23 cg24910161 5.043e-11 237.5
18438 HLA-B;HLA-C;XXbac-BPG248L24.12 6_25 cg09588770 0.000e+00 858.0
42089 MSH5;MSH5-SAPCD1 6_26 cg23634079 3.764e-01 309.0
30848 C2;ZBTB12 6_26 cg16505946 3.764e-01 309.0
13216 BTNL2 6_26 cg06871764 0.000e+00 397.3
44275 <NA> 6_26 cg24965496 0.000e+00 446.6
31319 HLA-DRA 6_26 cg16753237 0.000e+00 300.2
39715 <NA> 6_25 cg22110654 6.433e-10 796.6
PVE z num_eqtl
14343 1.418e-03 -37.22 1
46716 3.030e-04 -37.06 1
32508 5.330e-13 -30.92 1
31946 0.000e+00 28.80 1
41 0.000e+00 -28.48 1
6981 6.584e-13 28.44 1
6598 6.584e-13 28.44 1
9762 1.324e-19 -28.30 1
11743 6.875e-11 28.01 1
9784 0.000e+00 27.89 1
46204 4.983e-14 -27.87 1
26619 0.000e+00 -27.59 1
44201 3.418e-14 -27.47 1
18438 0.000e+00 27.12 1
42089 3.319e-04 26.92 1
30848 3.319e-04 -26.92 1
13216 0.000e+00 26.79 1
44275 0.000e+00 26.43 1
31319 0.000e+00 26.11 1
39715 1.462e-12 -25.85 1SNPs with highest PIPs
#snps with PIP>0.8 or 20 highest PIPs
head(ctwas_snp_res[order(-ctwas_snp_res$susie_pip),report_cols_snps],
max(sum(ctwas_snp_res$susie_pip>0.8), 20)) id region_tag id.1 susie_pip mu2 PVE
31705 rs6679677 1_70 rs6679677 1.0000 146.55 4.182e-04
58478 rs10803164 1_122 rs10803164 1.0000 186.85 5.331e-04
62820 rs12239046 1_131 rs12239046 1.0000 99.44 2.837e-04
115498 rs3835963 2_110 rs3835963 1.0000 107.56 3.069e-04
218483 rs1371794 4_51 rs1371794 1.0000 476.03 1.358e-03
221306 rs529050451 4_56 rs529050451 1.0000 708.60 2.022e-03
377037 rs56388170 7_24 rs56388170 1.0000 369.05 1.053e-03
396284 rs79912251 7_56 rs79912251 1.0000 145.07 4.139e-04
628523 rs79490353 13_7 rs79490353 1.0000 192.35 5.488e-04
777917 rs12461480 19_4 rs12461480 1.0000 215.36 6.145e-04
825443 rs13049759 21_24 rs13049759 1.0000 19341.21 5.519e-02
825445 rs13049893 21_24 rs13049893 1.0000 19430.21 5.544e-02
868195 rs34599082 1_78 rs34599082 1.0000 177.67 5.070e-04
934104 rs200599211 5_79 rs200599211 1.0000 1818.82 5.190e-03
979576 rs201369106 6_25 rs201369106 1.0000 12076.72 3.446e-02
1147212 rs4760 19_30 rs4760 1.0000 307.26 8.767e-04
72545 rs780093 2_16 rs780093 1.0000 137.29 3.917e-04
9489 rs3917932 1_22 rs3917932 1.0000 209.91 5.990e-04
396257 rs740047 7_56 rs740047 1.0000 84.84 2.421e-04
321991 rs41258084 6_27 rs41258084 1.0000 189.92 5.419e-04
958381 rs1233380 6_23 rs1233380 1.0000 223.44 6.376e-04
868194 rs12075 1_78 rs12075 1.0000 95.46 2.724e-04
437157 rs4738814 8_46 rs4738814 1.0000 235.41 6.717e-04
461756 rs7462429 8_92 rs7462429 1.0000 95.48 2.724e-04
427615 rs9644063 8_24 rs9644063 1.0000 80.16 2.287e-04
376898 rs177448 7_23 rs177448 1.0000 65.96 1.882e-04
979803 rs9267123 6_25 rs9267123 1.0000 869.07 2.480e-03
732773 rs9914577 17_3 rs9914577 1.0000 94.23 2.689e-04
613910 rs17041439 12_61 rs17041439 1.0000 51.74 1.476e-04
211431 rs218239 4_39 rs218239 1.0000 69.81 1.992e-04
974399 rs2524079 6_25 rs2524079 1.0000 2259.54 6.447e-03
301092 rs1042711 5_87 rs1042711 1.0000 47.90 1.367e-04
322031 rs73412964 6_27 rs73412964 1.0000 77.91 2.223e-04
63028 rs66858280 1_131 rs66858280 1.0000 50.47 1.440e-04
435508 rs140753685 8_42 rs140753685 1.0000 46.21 1.319e-04
576182 rs2852801 11_67 rs2852801 1.0000 50.90 1.452e-04
115472 rs77969163 2_109 rs77969163 1.0000 82.43 2.352e-04
716797 rs12926510 16_24 rs12926510 1.0000 125.48 3.580e-04
461695 rs56114972 8_92 rs56114972 1.0000 42.94 1.225e-04
617055 rs653178 12_67 rs653178 1.0000 573.76 1.637e-03
980873 rs2229094 6_25 rs2229094 1.0000 1485.75 4.239e-03
111332 rs2140046 2_102 rs2140046 1.0000 132.04 3.768e-04
584675 rs1800692 12_7 rs1800692 1.0000 40.22 1.147e-04
497983 rs115478735 9_70 rs115478735 1.0000 127.90 3.649e-04
806172 rs6072084 20_24 rs6072084 1.0000 74.43 2.124e-04
320540 rs1266074 6_26 rs1266074 1.0000 160.57 4.581e-04
379586 rs2700943 7_26 rs2700943 1.0000 53.33 1.522e-04
8108 rs4409706 1_20 rs4409706 1.0000 42.79 1.221e-04
353139 rs210942 6_89 rs210942 1.0000 68.49 1.954e-04
523143 rs748113 10_48 rs748113 1.0000 43.31 1.236e-04
777908 rs2041128 19_4 rs2041128 0.9999 163.61 4.668e-04
729549 rs11641197 16_49 rs11641197 0.9999 54.06 1.543e-04
523156 rs2166632 10_48 rs2166632 0.9999 38.01 1.084e-04
496491 rs13289095 9_66 rs13289095 0.9999 46.77 1.334e-04
379591 rs58130365 7_26 rs58130365 0.9999 40.61 1.159e-04
320502 rs17709192 6_21 rs17709192 0.9999 51.71 1.475e-04
751350 rs3826288 17_43 rs3826288 0.9999 45.77 1.306e-04
314127 rs630258 6_7 rs630258 0.9998 51.76 1.476e-04
221253 rs6814526 4_56 rs6814526 0.9998 309.12 8.818e-04
296841 rs4705986 5_80 rs4705986 0.9998 36.84 1.051e-04
770954 rs144596877 18_35 rs144596877 0.9998 35.03 9.994e-05
457576 rs60379390 8_85 rs60379390 0.9997 121.13 3.455e-04
766738 rs1025685 18_28 rs1025685 0.9997 53.87 1.537e-04
969114 rs3131063 6_24 rs3131063 0.9995 180.87 5.158e-04
720077 rs291040 16_30 rs291040 0.9995 43.56 1.242e-04
437188 rs3763591 8_46 rs3763591 0.9994 141.79 4.044e-04
609950 rs4842610 12_53 rs4842610 0.9993 73.64 2.100e-04
106994 rs59483741 2_91 rs59483741 0.9992 42.27 1.205e-04
506740 rs553304 10_14 rs553304 0.9992 35.45 1.011e-04
316759 rs1322599 6_13 rs1322599 0.9991 64.29 1.833e-04
406898 rs9649546 7_80 rs9649546 0.9986 47.87 1.364e-04
320525 rs2736155 6_26 rs2736155 0.9985 279.53 7.964e-04
406908 rs205721 7_80 rs205721 0.9984 35.96 1.024e-04
545506 rs7111092 11_7 rs7111092 0.9981 32.36 9.216e-05
442581 rs1430828 8_57 rs1430828 0.9981 33.93 9.663e-05
576191 rs238910 11_67 rs238910 0.9980 102.76 2.926e-04
656688 rs383599 13_62 rs383599 0.9980 47.36 1.349e-04
628525 rs7989654 13_7 rs7989654 0.9979 126.67 3.607e-04
806136 rs56206139 20_24 rs56206139 0.9975 32.74 9.319e-05
730241 rs72807046 16_50 rs72807046 0.9975 37.64 1.071e-04
617243 rs7970581 12_68 rs7970581 0.9975 32.75 9.320e-05
826077 rs390109 22_2 rs390109 0.9967 32.73 9.309e-05
25283 rs12130551 1_56 rs12130551 0.9966 31.80 9.042e-05
324927 rs11965885 6_33 rs11965885 0.9965 30.66 8.717e-05
360634 rs11759145 6_103 rs11759145 0.9963 34.94 9.933e-05
309233 rs2594836 5_104 rs2594836 0.9962 131.19 3.729e-04
301808 rs74995440 5_89 rs74995440 0.9955 29.79 8.461e-05
9492 rs3917912 1_22 rs3917912 0.9955 70.14 1.992e-04
1030785 rs14408 11_1 rs14408 0.9954 194.52 5.525e-04
584698 rs2286599 12_7 rs2286599 0.9953 77.11 2.190e-04
211458 rs723585 4_40 rs723585 0.9948 70.99 2.015e-04
791644 rs201074739 19_35 rs201074739 0.9945 30.16 8.559e-05
471562 rs2518722 9_16 rs2518722 0.9941 79.95 2.268e-04
202261 rs112783548 4_21 rs112783548 0.9937 28.71 8.141e-05
743011 rs68017435 17_26 rs68017435 0.9933 29.43 8.340e-05
734895 rs112315122 17_7 rs112315122 0.9932 35.19 9.972e-05
530091 rs17109928 10_60 rs17109928 0.9929 36.03 1.021e-04
423516 rs79690602 8_16 rs79690602 0.9925 27.74 7.856e-05
718211 rs7205341 16_27 rs7205341 0.9925 29.24 8.279e-05
10181 rs6690335 1_24 rs6690335 0.9922 41.18 1.166e-04
227127 rs35518360 4_67 rs35518360 0.9922 30.66 8.680e-05
227815 rs1548483 4_69 rs1548483 0.9919 41.53 1.176e-04
1054962 rs9332865 11_71 rs9332865 0.9918 41.12 1.164e-04
397773 rs1045916 7_60 rs1045916 0.9917 35.74 1.011e-04
695299 rs16947844 15_29 rs16947844 0.9916 70.18 1.986e-04
678759 rs67868394 14_46 rs67868394 0.9910 31.99 9.046e-05
125689 rs16858744 2_129 rs16858744 0.9906 29.89 8.447e-05
368103 rs2462661 7_9 rs2462661 0.9896 40.60 1.146e-04
475470 rs7042042 9_25 rs7042042 0.9895 27.47 7.755e-05
206382 rs75384208 4_30 rs75384208 0.9893 40.40 1.140e-04
483938 rs7863057 9_45 rs7863057 0.9882 43.22 1.219e-04
396361 rs7785869 7_57 rs7785869 0.9860 30.43 8.562e-05
2809 rs10864368 1_6 rs10864368 0.9844 36.92 1.037e-04
77564 rs10604697 2_26 rs10604697 0.9843 28.65 8.047e-05
82036 rs72804694 2_36 rs72804694 0.9842 33.03 9.275e-05
697841 rs876383 15_35 rs876383 0.9819 27.19 7.618e-05
1090478 rs138682554 15_42 rs138682554 0.9789 54.27 1.516e-04
753564 rs35967347 17_47 rs35967347 0.9786 33.03 9.223e-05
798683 rs1997814 20_8 rs1997814 0.9777 30.62 8.541e-05
171334 rs11721161 3_79 rs11721161 0.9767 40.57 1.131e-04
546677 rs4910421 11_9 rs4910421 0.9759 34.83 9.697e-05
188427 rs6782470 3_114 rs6782470 0.9755 26.41 7.350e-05
34996 rs512645 1_79 rs512645 0.9752 30.34 8.443e-05
868196 rs13962 1_78 rs13962 0.9752 58.56 1.630e-04
154686 rs17737336 3_48 rs17737336 0.9723 28.87 8.010e-05
377034 rs12113964 7_24 rs12113964 0.9719 36.67 1.017e-04
309184 rs10054235 5_104 rs10054235 0.9718 25.89 7.179e-05
742719 rs76714145 17_25 rs76714145 0.9712 29.08 8.059e-05
896157 rs17715343 2_97 rs17715343 0.9703 37.60 1.041e-04
775807 rs41506447 18_45 rs41506447 0.9702 25.37 7.022e-05
580061 rs34516251 11_80 rs34516251 0.9702 86.20 2.386e-04
748603 rs1801689 17_38 rs1801689 0.9697 25.62 7.087e-05
7235 rs10751725 1_19 rs10751725 0.9695 39.93 1.105e-04
105084 rs16858573 2_85 rs16858573 0.9690 81.52 2.254e-04
115491 rs155136 2_110 rs155136 0.9679 38.46 1.062e-04
666760 rs545787745 14_19 rs545787745 0.9678 25.20 6.959e-05
442541 rs56080040 8_56 rs56080040 0.9661 82.22 2.266e-04
742575 rs665268 17_25 rs665268 0.9657 42.98 1.184e-04
597984 rs80325942 12_30 rs80325942 0.9652 31.29 8.617e-05
868188 rs41264467 1_78 rs41264467 0.9647 37.87 1.043e-04
134685 rs35516956 3_3 rs35516956 0.9634 25.52 7.014e-05
572215 rs117594293 11_58 rs117594293 0.9629 28.74 7.897e-05
78782 rs11125040 2_28 rs11125040 0.9609 29.08 7.972e-05
787395 rs2194067 19_24 rs2194067 0.9586 28.64 7.833e-05
634076 rs2404726 13_19 rs2404726 0.9585 24.97 6.830e-05
399732 rs2470932 7_65 rs2470932 0.9572 25.09 6.852e-05
850036 rs182050989 1_18 rs182050989 0.9569 62.30 1.701e-04
35287 rs61804205 1_79 rs61804205 0.9557 57.99 1.581e-04
658620 rs9323580 14_4 rs9323580 0.9553 144.36 3.935e-04
655446 rs7991343 13_60 rs7991343 0.9548 26.98 7.352e-05
717874 rs34294937 16_27 rs34294937 0.9547 26.53 7.226e-05
557710 rs184267612 11_31 rs184267612 0.9541 28.69 7.809e-05
1157394 rs1015022 21_18 rs1015022 0.9540 47.98 1.306e-04
314121 rs585312 6_7 rs585312 0.9525 30.85 8.386e-05
407931 rs2347699 7_82 rs2347699 0.9490 31.56 8.545e-05
619609 rs76548188 12_74 rs76548188 0.9466 46.98 1.269e-04
952042 rs35789010 6_19 rs35789010 0.9459 81.40 2.197e-04
456525 rs12550442 8_83 rs12550442 0.9452 29.61 7.986e-05
58154 rs4626924 1_121 rs4626924 0.9447 47.84 1.290e-04
729892 rs7197027 16_50 rs7197027 0.9409 33.82 9.078e-05
794200 rs142236969 19_38 rs142236969 0.9407 25.08 6.731e-05
207362 rs4240247 4_31 rs4240247 0.9403 45.27 1.215e-04
339574 rs11757155 6_61 rs11757155 0.9389 51.60 1.382e-04
535580 rs76059302 10_70 rs76059302 0.9375 28.56 7.639e-05
320571 rs115487693 6_26 rs115487693 0.9372 182.55 4.882e-04
731521 rs111172648 16_53 rs111172648 0.9352 33.44 8.923e-05
620644 rs61955114 12_75 rs61955114 0.9350 38.34 1.023e-04
48861 rs10793741 1_104 rs10793741 0.9325 28.40 7.556e-05
49375 rs2724384 1_105 rs2724384 0.9323 95.42 2.538e-04
952603 rs74537235 6_22 rs74537235 0.9305 60.70 1.612e-04
484266 rs6479586 9_46 rs6479586 0.9282 24.23 6.416e-05
464528 rs10974716 9_5 rs10974716 0.9279 34.97 9.259e-05
607240 rs4842318 12_48 rs4842318 0.9278 28.28 7.488e-05
217915 rs7697091 4_50 rs7697091 0.9275 85.28 2.257e-04
412146 rs140190591 7_92 rs140190591 0.9267 25.21 6.666e-05
318103 rs10806918 6_15 rs10806918 0.9266 27.63 7.306e-05
582018 rs2017948 11_83 rs2017948 0.9265 23.83 6.300e-05
779131 rs4804815 19_7 rs4804815 0.9241 62.77 1.655e-04
319081 rs34492438 6_17 rs34492438 0.9234 25.42 6.698e-05
598993 rs3759178 12_32 rs3759178 0.9203 25.02 6.571e-05
422373 rs4386942 8_14 rs4386942 0.9195 32.48 8.521e-05
530143 rs61886179 10_61 rs61886179 0.9189 30.84 8.085e-05
928994 rs2853677 5_2 rs2853677 0.9180 39.92 1.046e-04
318840 rs115557837 6_16 rs115557837 0.9171 25.72 6.730e-05
711583 rs78083064 16_12 rs78083064 0.9147 23.78 6.207e-05
738239 rs941446 17_15 rs941446 0.9133 59.48 1.550e-04
292988 rs11064 5_72 rs11064 0.9099 53.21 1.381e-04
825829 rs760786796 22_2 rs760786796 0.9092 24.01 6.230e-05
746647 rs79979740 17_34 rs79979740 0.9088 33.53 8.694e-05
457606 rs35125576 8_85 rs35125576 0.9069 46.60 1.206e-04
464562 rs692503 9_5 rs692503 0.9062 47.68 1.233e-04
457053 rs4733814 8_84 rs4733814 0.9017 39.88 1.026e-04
321001 rs9391881 6_26 rs9391881 0.9015 520.45 1.339e-03
813816 rs3746372 20_37 rs3746372 0.9011 26.19 6.734e-05
602942 rs7968902 12_40 rs7968902 0.9009 48.61 1.250e-04
398310 rs60473539 7_62 rs60473539 0.8980 37.56 9.625e-05
921317 rs78065122 3_80 rs78065122 0.8954 36.17 9.240e-05
296486 rs144486602 5_78 rs144486602 0.8948 25.12 6.414e-05
497862 rs7045578 9_70 rs7045578 0.8913 27.17 6.911e-05
586594 rs12824533 12_11 rs12824533 0.8907 24.41 6.203e-05
457588 rs79584444 8_85 rs79584444 0.8902 49.33 1.253e-04
72570 rs9679004 2_16 rs9679004 0.8882 24.12 6.114e-05
780093 rs35639917 19_9 rs35639917 0.8874 55.35 1.401e-04
502035 rs10905634 10_7 rs10905634 0.8847 26.39 6.661e-05
367656 rs56703022 7_7 rs56703022 0.8837 28.94 7.296e-05
724897 rs12927351 16_39 rs12927351 0.8820 26.15 6.582e-05
421968 rs17151140 8_13 rs17151140 0.8813 29.13 7.325e-05
783175 rs34704748 19_15 rs34704748 0.8812 24.69 6.207e-05
5312 rs7546665 1_13 rs7546665 0.8804 26.76 6.721e-05
690873 rs2446407 15_21 rs2446407 0.8800 24.99 6.276e-05
690811 rs7169770 15_20 rs7169770 0.8758 28.06 7.012e-05
227861 rs7699743 4_69 rs7699743 0.8724 28.82 7.174e-05
207140 rs658080 4_31 rs658080 0.8715 26.22 6.519e-05
87324 rs7579497 2_47 rs7579497 0.8699 29.67 7.366e-05
782104 rs10420373 19_14 rs10420373 0.8687 57.96 1.437e-04
731657 rs57374020 16_53 rs57374020 0.8686 36.09 8.945e-05
828058 rs113934229 22_6 rs113934229 0.8681 26.68 6.608e-05
93325 rs1192820 2_59 rs1192820 0.8630 33.17 8.168e-05
853117 rs72683129 1_41 rs72683129 0.8626 70.63 1.738e-04
85826 rs1362478 2_44 rs1362478 0.8601 27.95 6.859e-05
77911 rs67584485 2_27 rs67584485 0.8596 36.97 9.068e-05
313944 rs201036 6_6 rs201036 0.8579 25.85 6.328e-05
814782 rs2823025 21_2 rs2823025 0.8536 26.60 6.478e-05
344433 rs9480643 6_71 rs9480643 0.8533 26.40 6.427e-05
396281 rs8 7_56 rs8 0.8503 30.18 7.322e-05
734864 rs9916791 17_7 rs9916791 0.8501 26.58 6.448e-05
20691 rs150467092 1_48 rs150467092 0.8498 25.93 6.288e-05
283260 rs7444298 5_52 rs7444298 0.8460 27.46 6.629e-05
375253 rs13229167 7_21 rs13229167 0.8420 40.04 9.620e-05
147697 rs11129979 3_31 rs11129979 0.8415 90.44 2.172e-04
808621 rs6095270 20_30 rs6095270 0.8399 152.74 3.661e-04
115481 rs36017642 2_109 rs36017642 0.8398 36.18 8.669e-05
807298 rs13043674 20_28 rs13043674 0.8377 26.13 6.246e-05
322383 rs34652732 6_29 rs34652732 0.8360 26.38 6.292e-05
840087 rs112682076 1_7 rs112682076 0.8349 35.20 8.385e-05
396277 rs17696150 7_56 rs17696150 0.8342 115.98 2.760e-04
948922 rs112655417 6_9 rs112655417 0.8337 6892.39 1.640e-02
604512 rs2137537 12_44 rs2137537 0.8337 24.96 5.937e-05
703724 rs899464 15_45 rs899464 0.8333 24.50 5.826e-05
26249 rs326664 1_59 rs326664 0.8332 25.93 6.165e-05
273793 rs149768957 5_32 rs149768957 0.8328 25.81 6.134e-05
644248 rs1330883 13_38 rs1330883 0.8325 27.49 6.531e-05
617064 rs117965634 12_67 rs117965634 0.8324 37.42 8.887e-05
603694 rs4913431 12_42 rs4913431 0.8308 29.79 7.063e-05
789513 rs559083563 19_29 rs559083563 0.8291 65.64 1.553e-04
521631 rs10997821 10_44 rs10997821 0.8282 32.30 7.634e-05
895772 rs75166367 2_97 rs75166367 0.8277 37.08 8.758e-05
161893 rs12493830 3_62 rs12493830 0.8255 30.87 7.272e-05
193168 rs66808687 4_2 rs66808687 0.8250 30.35 7.145e-05
695427 rs56906672 15_30 rs56906672 0.8234 26.56 6.239e-05
746953 rs148548662 17_34 rs148548662 0.8206 56.90 1.332e-04
38224 rs10753801 1_83 rs10753801 0.8206 24.58 5.756e-05
994761 rs3735485 7_33 rs3735485 0.8200 128.32 3.002e-04
510448 rs2807743 10_20 rs2807743 0.8175 122.29 2.853e-04
318422 rs6456418 6_15 rs6456418 0.8174 30.55 7.126e-05
368758 rs56195338 7_10 rs56195338 0.8154 43.70 1.017e-04
741296 rs12451746 17_21 rs12451746 0.8135 24.74 5.743e-05
825907 rs59667935 22_2 rs59667935 0.8133 25.65 5.952e-05
188346 rs720389 3_114 rs720389 0.8101 24.79 5.730e-05
464217 rs10733504 9_4 rs10733504 0.8099 28.00 6.471e-05
188464 rs6778003 3_114 rs6778003 0.8090 25.52 5.890e-05
955192 rs535876329 6_22 rs535876329 0.8048 35.81 8.223e-05
797951 rs117340493 20_7 rs117340493 0.8039 24.54 5.629e-05
274626 rs12658947 5_35 rs12658947 0.8005 39.89 9.111e-05
539260 rs17623606 10_78 rs17623606 0.8001 31.81 7.262e-05
z
31705 -12.1006
58478 -14.3656
62820 10.3814
115498 11.9370
218483 -23.3384
221306 1.6324
377037 20.7223
396284 -10.9517
628523 11.9357
777917 -7.6886
825443 4.9695
825445 4.8177
868195 -14.0113
934104 2.4536
979576 1.7190
1147212 -17.9363
72545 -11.9143
9489 -15.8760
396257 -7.1423
321991 12.3107
958381 19.2276
868194 6.0106
437157 -10.8946
461756 11.1057
427615 -9.2035
376898 2.6504
979803 -28.1821
732773 -10.4026
613910 7.2629
211431 8.2732
974399 32.3917
301092 -6.8138
322031 8.3367
63028 7.0545
435508 -7.0571
576182 6.9446
115472 9.1085
716797 11.5382
461695 -7.0784
617055 -26.3817
980873 19.4379
111332 10.5684
584675 -6.2056
497983 -11.9575
806172 9.2187
320540 13.1014
379586 5.4645
8108 7.7223
353139 -2.5202
523143 -7.3565
777908 -1.1756
729549 7.8304
523156 6.8721
496491 -6.7645
379591 -3.9061
320502 8.5293
751350 -6.3725
314127 7.6921
221253 -12.5319
296841 -5.1644
770954 -5.7062
457576 -13.9906
766738 7.5188
969114 -11.0071
720077 6.6988
437188 -9.7350
609950 -9.0244
106994 -6.6131
506740 5.8663
316759 -8.1734
406898 -7.0822
320525 20.5510
406908 6.0194
545506 4.9613
442581 -5.7235
576191 10.2585
656688 5.3312
628525 8.8376
806136 6.5292
730241 5.0321
617243 -5.3274
826077 -5.6685
25283 -5.5066
324927 -4.9938
360634 7.2656
309233 -12.8046
301808 -5.2876
9492 9.8609
1030785 15.8381
584698 8.8972
211458 -9.2632
791644 -3.9295
471562 -9.6543
202261 -5.2962
743011 -5.2449
734895 -5.8528
530091 2.5648
423516 -5.0532
718211 5.1851
10181 6.4568
227127 5.4852
227815 5.8609
1054962 6.6894
397773 -5.9039
695299 -8.5754
678759 5.8530
125689 -6.1809
368103 7.1263
475470 -4.5565
206382 6.3327
483938 -7.2362
396361 -5.2273
2809 7.3965
77564 4.2466
82036 5.6673
697841 -5.1295
1090478 6.6352
753564 5.3438
798683 -5.4026
171334 -6.2026
546677 -5.7716
188427 4.6439
34996 5.7613
868196 -4.9802
154686 -5.4082
377034 7.7822
309184 5.1875
742719 5.8237
896157 6.9180
775807 4.7579
580061 -10.0269
748603 4.7536
7235 -6.2659
105084 -8.7371
115491 8.2415
666760 -4.7561
442541 -9.4469
742575 7.4417
597984 -5.5136
868188 -4.8708
134685 -4.7395
572215 6.2129
78782 5.2992
787395 5.1593
634076 4.6345
399732 4.8593
850036 4.3921
35287 -8.1097
658620 10.8893
655446 -4.9404
717874 5.2069
557710 -5.3299
1157394 6.9349
314121 5.5926
407931 -5.5257
619609 -5.3471
952042 -9.7257
456525 5.3060
58154 7.0545
729892 -5.3814
794200 4.5892
207362 7.4784
339574 -7.5075
535580 -5.0133
320571 -5.8011
731521 5.4841
620644 6.4063
48861 -5.3338
49375 10.2518
952603 8.5058
484266 -4.4269
464528 -6.5608
607240 -5.2670
217915 -8.0809
412146 4.9752
318103 4.1644
582018 -4.5946
779131 -8.0320
319081 -4.7844
598993 4.6105
422373 6.6410
530143 -4.4662
928994 -7.6381
318840 5.0209
711583 3.8732
738239 -8.3444
292988 -7.5808
825829 4.4313
746647 -5.7245
457606 -6.9790
464562 7.5243
457053 7.7217
321001 29.7491
813816 -4.8715
602942 6.8687
398310 -3.9742
921317 -6.1001
296486 -4.8858
497862 5.2746
586594 4.5310
457588 -6.2508
72570 3.3681
780093 -9.5115
502035 4.8594
367656 5.3596
724897 4.7348
421968 3.0103
783175 4.2712
5312 4.8663
690873 4.7005
690811 -2.9983
227861 -4.4658
207140 -4.4771
87324 -5.2861
782104 -9.2524
731657 -5.6078
828058 -5.3105
93325 5.5006
853117 12.7746
85826 4.9226
77911 -6.1157
313944 4.5511
814782 5.1986
344433 4.7105
396281 4.9715
734864 4.3527
20691 4.5431
283260 -4.8603
375253 6.5229
147697 -10.1402
808621 1.4297
115481 -1.8327
807298 -4.6724
322383 4.3281
840087 -6.3056
396277 -11.6557
948922 -0.3897
604512 -4.7285
703724 -4.5188
26249 4.8992
273793 -5.0365
644248 -4.5407
617064 -7.5514
603694 -5.3758
789513 8.2187
521631 -5.4996
895772 -6.3367
161893 5.2481
193168 5.1512
695427 -4.5684
746953 7.6171
38224 -4.3837
994761 11.7187
510448 11.5079
318422 -5.4925
368758 -6.4972
741296 4.5802
825907 5.0353
188346 -4.0308
464217 -4.1988
188464 -4.5603
955192 5.8186
797951 -3.8163
274626 5.9971
539260 5.9897SNPs with largest effect sizes
#plot PIP vs effect size
#plot(ctwas_snp_res$susie_pip, ctwas_snp_res$mu2, xlab="PIP", ylab="mu^2", main="SNP PIPs vs Effect Size")
#SNPs with 50 largest effect sizes
head(ctwas_snp_res[order(-ctwas_snp_res$mu2),report_cols_snps],50) id region_tag id.1 susie_pip mu2 PVE z
825445 rs13049893 21_24 rs13049893 1.000e+00 19430 5.544e-02 4.818
825443 rs13049759 21_24 rs13049759 1.000e+00 19341 5.519e-02 4.970
825430 rs13052701 21_24 rs13052701 0.000e+00 16370 0.000e+00 4.944
825433 rs147757092 21_24 rs147757092 0.000e+00 14934 0.000e+00 4.614
825476 rs11702800 21_24 rs11702800 0.000e+00 14349 0.000e+00 -5.560
825489 rs2268523 21_24 rs2268523 0.000e+00 14313 0.000e+00 -5.586
825486 rs9981445 21_24 rs9981445 0.000e+00 14077 0.000e+00 -5.570
825506 rs2839257 21_24 rs2839257 0.000e+00 13981 0.000e+00 -5.710
825470 rs11909986 21_24 rs11909986 0.000e+00 12579 0.000e+00 6.006
825424 rs35679325 21_24 rs35679325 0.000e+00 12250 0.000e+00 -5.090
825441 rs4819221 21_24 rs4819221 0.000e+00 12208 0.000e+00 5.060
979573 rs3869130 6_25 rs3869130 3.125e-01 12143 1.083e-02 14.055
979574 rs3869131 6_25 rs3869131 1.870e-01 12143 6.479e-03 14.047
979570 rs3899823 6_25 rs3899823 4.284e-01 12142 1.484e-02 14.063
979586 rs34259803 6_25 rs34259803 4.423e-02 12140 1.532e-03 14.034
979571 rs3869129 6_25 rs3869129 2.788e-02 12136 9.653e-04 14.056
825449 rs4818832 21_24 rs4818832 0.000e+00 12119 0.000e+00 5.082
825448 rs62226478 21_24 rs62226478 0.000e+00 12116 0.000e+00 5.087
979563 rs73404245 6_25 rs73404245 5.850e-08 12100 2.020e-09 13.998
825446 rs34586434 21_24 rs34586434 0.000e+00 12094 0.000e+00 5.094
979576 rs201369106 6_25 rs201369106 1.000e+00 12077 3.446e-02 1.719
979582 rs7769942 6_25 rs7769942 8.882e-16 11984 3.037e-17 14.605
979560 rs566631013 6_25 rs566631013 0.000e+00 11108 0.000e+00 12.820
979558 rs373478096 6_25 rs373478096 0.000e+00 11108 0.000e+00 12.820
979559 rs200256874 6_25 rs200256874 0.000e+00 11108 0.000e+00 12.820
825437 rs2032226 21_24 rs2032226 0.000e+00 10457 0.000e+00 5.361
825431 rs4535149 21_24 rs4535149 0.000e+00 10369 0.000e+00 5.360
979218 rs9501109 6_25 rs9501109 0.000e+00 10123 0.000e+00 16.607
825421 rs2001809 21_24 rs2001809 0.000e+00 9906 0.000e+00 3.733
979285 rs60539855 6_25 rs60539855 0.000e+00 9532 0.000e+00 16.465
979652 rs4458721 6_25 rs4458721 0.000e+00 9423 0.000e+00 16.419
979588 rs73404265 6_25 rs73404265 0.000e+00 9172 0.000e+00 13.695
979581 rs7769403 6_25 rs7769403 0.000e+00 9171 0.000e+00 13.693
825426 rs4819218 21_24 rs4819218 0.000e+00 8965 0.000e+00 4.926
825425 rs2280959 21_24 rs2280959 0.000e+00 8953 0.000e+00 4.934
825511 rs2073381 21_24 rs2073381 0.000e+00 8897 0.000e+00 4.936
979330 rs117813801 6_25 rs117813801 0.000e+00 8779 0.000e+00 13.870
979360 rs114921825 6_25 rs114921825 0.000e+00 8779 0.000e+00 13.705
979331 rs143741838 6_25 rs143741838 0.000e+00 8779 0.000e+00 13.871
979355 rs4090415 6_25 rs4090415 0.000e+00 8774 0.000e+00 13.768
979353 rs4090417 6_25 rs4090417 0.000e+00 8773 0.000e+00 13.767
979354 rs4090416 6_25 rs4090416 0.000e+00 8773 0.000e+00 13.767
979351 rs9501116 6_25 rs9501116 0.000e+00 8773 0.000e+00 13.764
979350 rs9501115 6_25 rs9501115 0.000e+00 8772 0.000e+00 13.765
979555 rs28575156 6_25 rs28575156 0.000e+00 8768 0.000e+00 13.707
979388 rs2394999 6_25 rs2394999 0.000e+00 8765 0.000e+00 13.725
979382 rs2894212 6_25 rs2894212 0.000e+00 8765 0.000e+00 13.727
979384 rs4631325 6_25 rs4631325 0.000e+00 8765 0.000e+00 13.727
979387 rs2394998 6_25 rs2394998 0.000e+00 8765 0.000e+00 13.725
979380 rs80339222 6_25 rs80339222 0.000e+00 8765 0.000e+00 13.726SNPs with highest PVE
#SNPs with 50 highest pve
head(ctwas_snp_res[order(-ctwas_snp_res$PVE),report_cols_snps],50) id region_tag id.1 susie_pip mu2 PVE z
825445 rs13049893 21_24 rs13049893 1.00000 19430.2 0.0554404 4.8177
825443 rs13049759 21_24 rs13049759 1.00000 19341.2 0.0551865 4.9695
979576 rs201369106 6_25 rs201369106 1.00000 12076.7 0.0344586 1.7190
948922 rs112655417 6_9 rs112655417 0.83369 6892.4 0.0163954 -0.3897
979570 rs3899823 6_25 rs3899823 0.42840 12142.4 0.0148423 14.0629
948881 rs470863 6_9 rs470863 0.56473 6885.3 0.0110945 -0.4829
979573 rs3869130 6_25 rs3869130 0.31250 12143.2 0.0108276 14.0552
948894 rs470562 6_9 rs470562 0.41950 6885.7 0.0082420 -0.4744
979574 rs3869131 6_25 rs3869131 0.18699 12143.2 0.0064790 14.0471
974399 rs2524079 6_25 rs2524079 1.00000 2259.5 0.0064472 32.3917
934104 rs200599211 5_79 rs200599211 1.00000 1818.8 0.0051897 2.4536
980873 rs2229094 6_25 rs2229094 0.99999 1485.7 0.0042392 19.4379
979803 rs9267123 6_25 rs9267123 1.00000 869.1 0.0024797 -28.1821
948948 rs112850802 6_9 rs112850802 0.12491 6876.9 0.0024510 -0.3953
221306 rs529050451 4_56 rs529050451 1.00000 708.6 0.0020219 1.6324
617055 rs653178 12_67 rs653178 0.99999 573.8 0.0016371 -26.3817
979586 rs34259803 6_25 rs34259803 0.04423 12140.2 0.0015322 14.0343
218483 rs1371794 4_51 rs1371794 1.00000 476.0 0.0013583 -23.3384
321001 rs9391881 6_26 rs9391881 0.90152 520.4 0.0013388 29.7491
377037 rs56388170 7_24 rs56388170 1.00000 369.0 0.0010530 20.7223
979571 rs3869129 6_25 rs3869129 0.02788 12135.9 0.0009653 14.0556
221253 rs6814526 4_56 rs6814526 0.99979 309.1 0.0008818 -12.5319
1147212 rs4760 19_30 rs4760 1.00000 307.3 0.0008767 -17.9363
221309 rs9654217 4_56 rs9654217 0.42939 712.0 0.0008723 7.1517
221310 rs9654218 4_56 rs9654218 0.42509 712.0 0.0008636 7.1513
320525 rs2736155 6_26 rs2736155 0.99854 279.5 0.0007964 20.5510
437157 rs4738814 8_46 rs4738814 1.00000 235.4 0.0006717 -10.8946
969543 rs1264349 6_24 rs1264349 0.45458 502.0 0.0006511 -24.7873
958381 rs1233380 6_23 rs1233380 1.00000 223.4 0.0006376 19.2276
320477 rs67040724 6_21 rs67040724 0.71988 307.4 0.0006315 -18.4527
777917 rs12461480 19_4 rs12461480 1.00000 215.4 0.0006145 -7.6886
9489 rs3917932 1_22 rs3917932 1.00000 209.9 0.0005990 -15.8760
934118 rs13361914 5_79 rs13361914 0.10966 1809.9 0.0005663 -1.7542
1030785 rs14408 11_1 rs14408 0.99545 194.5 0.0005525 15.8381
934125 rs77753417 5_79 rs77753417 0.10675 1809.9 0.0005513 -1.7544
628523 rs79490353 13_7 rs79490353 1.00000 192.4 0.0005488 11.9357
321991 rs41258084 6_27 rs41258084 1.00000 189.9 0.0005419 12.3107
58478 rs10803164 1_122 rs10803164 1.00000 186.8 0.0005331 -14.3656
353114 rs56293029 6_89 rs56293029 0.60434 305.0 0.0005260 -16.9971
934121 rs113694337 5_79 rs113694337 0.10124 1809.8 0.0005228 -1.7519
509026 rs112955547 10_18 rs112955547 0.47367 385.0 0.0005203 -18.4434
969114 rs3131063 6_24 rs3131063 0.99952 180.9 0.0005158 -11.0071
868195 rs34599082 1_78 rs34599082 1.00000 177.7 0.0005070 -14.0113
321920 rs9276625 6_27 rs9276625 0.54185 327.5 0.0005064 -20.9363
958798 rs3131894 6_23 rs3131894 0.55281 314.4 0.0004960 -23.1028
320571 rs115487693 6_26 rs115487693 0.93719 182.6 0.0004882 -5.8011
948952 rs72819781 6_9 rs72819781 0.02476 6862.6 0.0004848 -0.4151
777908 rs2041128 19_4 rs2041128 0.99993 163.6 0.0004668 -1.1756
320540 rs1266074 6_26 rs1266074 0.99997 160.6 0.0004581 13.1014
963740 rs9260620 6_24 rs9260620 0.56272 276.7 0.0004442 -21.7153SNPs with largest z scores
#histogram of (abs) SNP z scores
hist(abs(ctwas_snp_res$z))
#SNPs with 50 largest z scores
head(ctwas_snp_res[order(-abs(ctwas_snp_res$z)),report_cols_snps],50) id region_tag id.1 susie_pip mu2 PVE z
1108383 rs8078723 17_23 rs8078723 2.011e-03 608.4 3.491e-06 37.33
1108420 rs709592 17_23 rs709592 2.349e-03 609.6 4.085e-06 37.32
1108421 rs709591 17_23 rs709591 1.994e-03 608.9 3.465e-06 37.31
1108375 rs55771023 17_23 rs55771023 1.504e-03 607.4 2.607e-06 37.30
1108374 rs55736351 17_23 rs55736351 1.422e-03 607.2 2.463e-06 37.30
1108339 rs4795414 17_23 rs4795414 1.028e-03 605.6 1.776e-06 37.30
1108340 rs4795415 17_23 rs4795415 1.026e-03 605.6 1.774e-06 37.30
1108341 rs4795416 17_23 rs4795416 1.021e-03 605.5 1.765e-06 37.30
1108350 rs8065519 17_23 rs8065519 1.019e-03 605.6 1.760e-06 37.30
1108335 rs56922390 17_23 rs56922390 9.628e-04 605.3 1.663e-06 37.29
1108361 rs12602172 17_23 rs12602172 9.388e-04 605.5 1.622e-06 37.29
1108334 rs4794822 17_23 rs4794822 8.848e-04 605.1 1.528e-06 37.29
1108369 rs55846942 17_23 rs55846942 9.324e-04 605.5 1.611e-06 37.29
1108359 rs12600856 17_23 rs12600856 9.182e-04 605.4 1.586e-06 37.29
1108380 rs4795419 17_23 rs4795419 9.409e-04 605.6 1.626e-06 37.29
1108381 rs4794823 17_23 rs4794823 8.888e-04 605.4 1.535e-06 37.29
1108353 rs8070454 17_23 rs8070454 8.040e-04 604.9 1.388e-06 37.29
1108372 rs4795418 17_23 rs4795418 8.301e-04 605.2 1.433e-06 37.29
1108355 rs6503530 17_23 rs6503530 7.779e-04 604.8 1.342e-06 37.28
1108376 rs7221894 17_23 rs7221894 7.095e-04 604.6 1.224e-06 37.28
1108417 rs2227336 17_23 rs2227336 6.848e-04 604.9 1.182e-06 37.27
1108404 rs2227322 17_23 rs2227322 6.025e-04 604.4 1.039e-06 37.27
1108415 rs1042658 17_23 rs1042658 6.174e-04 604.5 1.065e-06 37.27
1108425 rs11871747 17_23 rs11871747 5.111e-04 605.3 8.826e-07 37.26
1108393 rs7208815 17_23 rs7208815 5.882e-04 604.3 1.014e-06 37.26
1108386 rs4795420 17_23 rs4795420 4.990e-04 603.6 8.594e-07 37.26
1108385 rs62065177 17_23 rs62065177 4.922e-04 603.5 8.477e-07 37.26
1108395 rs7214085 17_23 rs7214085 4.746e-04 603.4 8.172e-07 37.26
1108390 rs57065891 17_23 rs57065891 4.714e-04 603.4 8.117e-07 37.26
1108398 rs59925331 17_23 rs59925331 4.691e-04 603.4 8.076e-07 37.26
1108399 rs2227315 17_23 rs2227315 4.407e-04 603.2 7.584e-07 37.25
1108326 rs7021 17_23 rs7021 3.290e-04 601.4 5.646e-07 37.24
1108317 rs4795412 17_23 rs4795412 2.895e-04 600.8 4.963e-07 37.23
1108330 rs8081692 17_23 rs8081692 2.921e-04 601.0 5.010e-07 37.23
1108293 rs57968500 17_23 rs57968500 2.284e-04 599.5 3.907e-07 37.22
1108432 rs4794824 17_23 rs4794824 1.008e-04 600.6 1.727e-07 37.13
1108430 rs3213762 17_23 rs3213762 2.695e-05 595.3 4.578e-08 37.07
1108356 rs111848559 17_23 rs111848559 5.049e-05 596.4 8.592e-08 37.06
1108447 rs6503533 17_23 rs6503533 1.088e-05 605.6 1.879e-08 -36.96
1108316 rs3826331 17_23 rs3826331 3.769e-09 580.5 6.242e-12 -36.93
1108418 rs1045929 17_23 rs1045929 1.595e-06 586.9 2.671e-09 36.89
1108304 rs60666652 17_23 rs60666652 2.155e-07 582.8 3.583e-10 36.72
1108303 rs60082402 17_23 rs60082402 2.021e-07 582.6 3.360e-10 36.72
1108389 rs60005225 17_23 rs60005225 4.537e-08 577.5 7.476e-11 36.67
1108347 rs12941811 17_23 rs12941811 7.362e-12 582.0 1.222e-14 -36.55
1108321 rs8070444 17_23 rs8070444 3.087e-11 578.5 5.095e-14 -35.99
1108289 rs12450688 17_23 rs12450688 3.433e-11 581.0 5.691e-14 -35.98
1108272 rs2305482 17_23 rs2305482 4.329e-11 583.2 7.204e-14 -35.98
1108322 rs8071037 17_23 rs8071037 2.883e-11 576.9 4.746e-14 -35.97
1108292 rs9915252 17_23 rs9915252 3.184e-11 579.3 5.263e-14 -35.96
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cowplot_1.1.1 ggplot2_3.4.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.35 bslib_0.4.1 generics_0.1.3
[5] colorspace_2.0-3 vctrs_0.5.1 htmltools_0.5.4 yaml_2.3.6
[9] utf8_1.2.2 blob_1.2.3 rlang_1.0.6 jquerylib_0.1.4
[13] later_1.3.0 pillar_1.8.1 withr_2.5.0 glue_1.6.2
[17] DBI_1.1.3 bit64_4.0.5 lifecycle_1.0.3 stringr_1.5.0
[21] munsell_0.5.0 gtable_0.3.1 evaluate_0.19 memoise_2.0.1
[25] labeling_0.4.2 knitr_1.41 callr_3.7.3 fastmap_1.1.0
[29] httpuv_1.6.7 ps_1.7.2 fansi_1.0.3 highr_0.9
[33] Rcpp_1.0.9 promises_1.2.0.1 scales_1.2.1 cachem_1.0.6
[37] jsonlite_1.8.4 farver_2.1.0 fs_1.5.2 bit_4.0.5
[41] digest_0.6.31 stringi_1.7.8 processx_3.8.0 dplyr_1.0.10
[45] getPass_0.2-2 rprojroot_2.0.3 grid_4.1.0 cli_3.4.1
[49] tools_4.1.0 magrittr_2.0.3 sass_0.4.4 tibble_3.1.8
[53] RSQLite_2.2.19 whisker_0.4.1 pkgconfig_2.0.3 data.table_1.14.6
[57] assertthat_0.2.1 rmarkdown_2.19 httr_1.4.4 rstudioapi_0.14
[61] R6_2.5.1 git2r_0.30.1 compiler_4.1.0