Atrial fibrillation - Heart Atrial Appendage
sheng Qian
2021-12-18
Last updated: 2022-02-11
Checks: 6 1
Knit directory: cTWAS_analysis/
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Weight QC
[1] 10862
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1103 776 625 427 501 624 518 377 399 423 648 611 203 368 356 495
17 18 19 20 21 22
676 177 840 318 126 271 [1] 7113[1] 0.65485Load ctwas results
Check convergence of parameters
********************************************************Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute:
theme_set(theme_cowplot())********************************************************
gene snp
0.02084875 0.00019279 gene snp
9.6465 8.6791 [1] 1030836[1] 10862 6839050 gene snp
0.0021192 0.0111008 [1] 0.012251 0.125239Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_eqtl
2293 CAV1 7_70 1.00000 622.848 6.0422e-04 15.5679 3
3275 PRRX1 1_84 0.99988 119.347 1.1576e-04 14.6676 2
4009 DEK 6_14 0.99251 63.478 6.1118e-05 -9.0000 1
3527 CCND2 12_4 0.99062 27.016 2.5962e-05 -5.2838 1
1310 PXN 12_75 0.98265 29.472 2.8094e-05 -5.3283 1
12836 RP11-325L7.2 5_82 0.98260 1993.738 1.9004e-03 12.3563 1
9257 AGAP5 10_49 0.97792 48.915 4.6404e-05 11.5186 2
3523 KLF12 13_36 0.97708 26.000 2.4644e-05 -5.0725 1
6621 AKAP6 14_8 0.97215 76.818 7.2446e-05 -9.1974 1
6914 JAM2 21_9 0.96405 22.193 2.0755e-05 4.5632 2
9639 DLEU1 13_21 0.95865 23.591 2.1939e-05 4.6971 1
11818 DPF3 14_34 0.95743 33.355 3.0980e-05 6.2650 3
10521 FAM43A 3_120 0.95692 29.699 2.7569e-05 -5.4872 1
2444 SEC23IP 10_74 0.95178 22.389 2.0672e-05 -4.5652 2
13075 LINC01629 14_36 0.94716 31.886 2.9298e-05 -5.6957 1
2138 AES 19_4 0.94032 20.204 1.8430e-05 4.1828 3
4658 POPDC3 6_70 0.92525 25.195 2.2614e-05 -4.7582 1
10290 NKX2-5 5_103 0.92287 61.560 5.5112e-05 -9.3919 1
7515 TNFSF13 17_7 0.91352 34.270 3.0370e-05 -5.8831 1
5185 GYPC 2_74 0.90681 38.959 3.4271e-05 -6.3805 1
8248 CMTM5 14_3 0.90673 30.098 2.6474e-05 -5.4727 1
10548 SCN10A 3_28 0.88676 77.720 6.6858e-05 -8.8143 1
13967 RP5-890E16.5 17_28 0.86606 23.112 1.9418e-05 -4.7612 1
712 SP100 2_135 0.86587 18.735 1.5737e-05 -3.6713 2
9012 MTSS1 8_82 0.85941 20.879 1.7407e-05 4.4026 2
8992 MURC 9_50 0.84789 23.347 1.9204e-05 4.9120 2
5223 PSMB7 9_64 0.84307 25.301 2.0692e-05 -4.8209 1
6114 STK11IP 2_130 0.84064 18.968 1.5468e-05 -3.8680 2
10416 PGP 16_2 0.82986 28.512 2.2953e-05 5.9438 1
9691 BOK 2_144 0.82560 19.183 1.5363e-05 3.9101 3
8420 MARS 12_36 0.81803 17.820 1.4141e-05 -3.3662 1
3088 GNB4 3_110 0.80977 30.346 2.3838e-05 -5.5833 1Genes with largest effect sizes
genename region_tag susie_pip mu2 PVE z num_eqtl
3250 WIPF1 2_105 0.0000e+00 2852.25 0.0000e+00 8.44156 1
12836 RP11-325L7.2 5_82 9.8260e-01 1993.74 1.9004e-03 12.35632 1
1487 SIRT1 10_44 3.3372e-01 1299.24 4.2062e-04 -5.05385 1
7413 IL6R 1_75 5.8624e-12 1273.18 7.2406e-15 -4.97849 1
6444 HERC4 10_44 1.0134e-01 1220.94 1.2003e-04 -5.35956 2
11106 NACA 12_35 5.1277e-03 1179.06 5.8650e-06 -6.24081 2
960 BAZ2A 12_35 2.0473e-03 1162.56 2.3089e-06 -5.94286 1
7986 SLC35A1 6_59 0.0000e+00 804.88 0.0000e+00 -5.07246 1
2507 WNT3 17_27 3.7072e-05 797.46 2.8679e-08 -4.38940 2
2292 CAV2 7_70 0.0000e+00 689.11 0.0000e+00 14.53494 2
2293 CAV1 7_70 1.0000e+00 622.85 6.0422e-04 15.56787 3
4999 ORC3 6_59 0.0000e+00 597.60 0.0000e+00 4.16667 1
10616 ARL17A 17_27 7.7139e-06 488.69 3.6569e-09 -0.53995 2
3687 KDM3B 5_82 5.2760e-06 436.26 2.2328e-09 -6.62873 2
7728 GPR155 2_105 0.0000e+00 371.93 0.0000e+00 -1.45466 2
7276 ARHGAP27 17_27 5.8760e-06 189.44 1.0799e-09 0.15765 2
10739 MAPT 17_27 2.7912e-04 166.51 4.5087e-08 3.87246 2
7729 PMVK 1_76 9.6933e-05 161.15 1.5153e-08 -12.10294 1
7730 PBXIP1 1_76 9.3359e-05 156.14 1.4141e-08 -11.86765 1
341 FAM13B 5_82 1.8264e-01 153.98 2.7282e-05 7.60092 2Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_eqtl
12836 RP11-325L7.2 5_82 0.98260 1993.738 1.9004e-03 12.3563 1
2293 CAV1 7_70 1.00000 622.848 6.0422e-04 15.5679 3
1487 SIRT1 10_44 0.33372 1299.241 4.2062e-04 -5.0538 1
6444 HERC4 10_44 0.10134 1220.940 1.2003e-04 -5.3596 2
3275 PRRX1 1_84 0.99988 119.347 1.1576e-04 14.6676 2
6621 AKAP6 14_8 0.97215 76.818 7.2446e-05 -9.1974 1
10548 SCN10A 3_28 0.88676 77.720 6.6858e-05 -8.8143 1
12013 ZSWIM8 10_49 0.75224 87.260 6.3677e-05 -11.2165 1
4009 DEK 6_14 0.99251 63.478 6.1118e-05 -9.0000 1
8298 SYNPO2L 10_49 0.62657 99.725 6.0615e-05 -11.9457 1
10290 NKX2-5 5_103 0.92287 61.560 5.5112e-05 -9.3919 1
9257 AGAP5 10_49 0.97792 48.915 4.6404e-05 11.5186 2
5185 GYPC 2_74 0.90681 38.959 3.4271e-05 -6.3805 1
3665 KCNJ5 11_80 0.50375 67.733 3.3100e-05 -8.7481 1
11818 DPF3 14_34 0.95743 33.355 3.0980e-05 6.2650 3
10515 C5orf47 5_104 0.76613 41.611 3.0926e-05 6.6806 1
7515 TNFSF13 17_7 0.91352 34.270 3.0370e-05 -5.8831 1
13075 LINC01629 14_36 0.94716 31.886 2.9298e-05 -5.6957 1
1310 PXN 12_75 0.98265 29.472 2.8094e-05 -5.3283 1
10521 FAM43A 3_120 0.95692 29.699 2.7569e-05 -5.4872 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z num_eqtl
2293 CAV1 7_70 1.0000e+00 622.848 6.0422e-04 15.5679 3
3275 PRRX1 1_84 9.9988e-01 119.347 1.1576e-04 14.6676 2
2292 CAV2 7_70 0.0000e+00 689.112 0.0000e+00 14.5349 2
12836 RP11-325L7.2 5_82 9.8260e-01 1993.738 1.9004e-03 12.3563 1
7729 PMVK 1_76 9.6933e-05 161.146 1.5153e-08 -12.1029 1
8298 SYNPO2L 10_49 6.2657e-01 99.725 6.0615e-05 -11.9457 1
7730 PBXIP1 1_76 9.3359e-05 156.141 1.4141e-08 -11.8676 1
9805 MYOZ1 10_49 3.4978e-03 88.984 3.0193e-07 11.7593 2
9257 AGAP5 10_49 9.7792e-01 48.915 4.6404e-05 11.5186 2
12013 ZSWIM8 10_49 7.5224e-01 87.260 6.3677e-05 -11.2165 1
6395 C9orf3 9_48 4.9199e-02 94.742 4.5218e-06 10.6716 1
7407 ZBTB7B 1_76 9.6366e-05 122.095 1.1414e-08 10.6389 1
13556 RP1-79C4.4 1_84 8.2542e-03 58.951 4.7204e-07 9.5864 2
10290 NKX2-5 5_103 9.2287e-01 61.560 5.5112e-05 -9.3919 1
9719 SEC24C 10_49 9.5972e-04 46.261 4.3069e-08 9.2719 2
6621 AKAP6 14_8 9.7215e-01 76.818 7.2446e-05 -9.1974 1
4009 DEK 6_14 9.9251e-01 63.478 6.1118e-05 -9.0000 1
10548 SCN10A 3_28 8.8676e-01 77.720 6.6858e-05 -8.8143 1
3665 KCNJ5 11_80 5.0375e-01 67.733 3.3100e-05 -8.7481 1
7733 DCST2 1_76 2.6132e-04 89.760 2.2754e-08 -8.7183 1Comparing z scores and PIPs
[1] 0.008654 genename region_tag susie_pip mu2 PVE z num_eqtl
2293 CAV1 7_70 1.0000e+00 622.848 6.0422e-04 15.5679 3
3275 PRRX1 1_84 9.9988e-01 119.347 1.1576e-04 14.6676 2
2292 CAV2 7_70 0.0000e+00 689.112 0.0000e+00 14.5349 2
12836 RP11-325L7.2 5_82 9.8260e-01 1993.738 1.9004e-03 12.3563 1
7729 PMVK 1_76 9.6933e-05 161.146 1.5153e-08 -12.1029 1
8298 SYNPO2L 10_49 6.2657e-01 99.725 6.0615e-05 -11.9457 1
7730 PBXIP1 1_76 9.3359e-05 156.141 1.4141e-08 -11.8676 1
9805 MYOZ1 10_49 3.4978e-03 88.984 3.0193e-07 11.7593 2
9257 AGAP5 10_49 9.7792e-01 48.915 4.6404e-05 11.5186 2
12013 ZSWIM8 10_49 7.5224e-01 87.260 6.3677e-05 -11.2165 1
6395 C9orf3 9_48 4.9199e-02 94.742 4.5218e-06 10.6716 1
7407 ZBTB7B 1_76 9.6366e-05 122.095 1.1414e-08 10.6389 1
13556 RP1-79C4.4 1_84 8.2542e-03 58.951 4.7204e-07 9.5864 2
10290 NKX2-5 5_103 9.2287e-01 61.560 5.5112e-05 -9.3919 1
9719 SEC24C 10_49 9.5972e-04 46.261 4.3069e-08 9.2719 2
6621 AKAP6 14_8 9.7215e-01 76.818 7.2446e-05 -9.1974 1
4009 DEK 6_14 9.9251e-01 63.478 6.1118e-05 -9.0000 1
10548 SCN10A 3_28 8.8676e-01 77.720 6.6858e-05 -8.8143 1
3665 KCNJ5 11_80 5.0375e-01 67.733 3.3100e-05 -8.7481 1
7733 DCST2 1_76 2.6132e-04 89.760 2.2754e-08 -8.7183 1SNPs with highest PIPs
id region_tag susie_pip mu2 PVE z
28439 rs12404927 1_75 1.00000 1437.877 1.3949e-03 -1.55172
28440 rs7536152 1_75 1.00000 1473.019 1.4290e-03 -6.46269
28533 rs34515871 1_76 1.00000 299.284 2.9033e-04 17.00000
32410 rs12142529 1_83 1.00000 145.613 1.4126e-04 12.03960
32435 rs112797273 1_83 1.00000 101.671 9.8629e-05 9.49038
183533 rs1906615 4_72 1.00000 1756.731 1.7042e-03 45.16049
183538 rs7440714 4_72 1.00000 992.101 9.6242e-04 -9.21834
272612 rs111990232 6_59 1.00000 1710.909 1.6597e-03 0.53927
414968 rs76106073 10_44 1.00000 1273.722 1.2356e-03 0.65722
550561 rs140798119 15_35 1.00000 285.261 2.7673e-04 3.99507
550564 rs74022964 15_35 1.00000 342.922 3.3266e-04 12.57778
681435 rs4972703 2_105 1.00000 4299.785 4.1712e-03 -0.78427
739005 rs9770220 7_70 1.00000 835.769 8.1077e-04 -5.28148
788780 rs61937778 12_35 1.00000 1668.550 1.6186e-03 -1.30570
28537 rs2878412 1_76 1.00000 105.575 1.0242e-04 5.42500
586354 rs62056842 17_27 1.00000 1130.219 1.0964e-03 1.12690
28535 rs11576820 1_76 1.00000 133.716 1.2972e-04 8.02439
422177 rs60469668 10_66 1.00000 172.108 1.6696e-04 16.96471
110779 rs9852222 3_9 1.00000 83.843 8.1335e-05 8.38235
339255 rs373983 8_21 1.00000 67.643 6.5620e-05 8.55882
298378 rs12112152 7_15 1.00000 45.134 4.3784e-05 6.93590
422175 rs7094488 10_66 1.00000 110.014 1.0672e-04 14.10606
28540 rs10908445 1_76 1.00000 193.570 1.8778e-04 -13.14706
570907 rs6499606 16_39 1.00000 103.941 1.0083e-04 12.63768
826958 rs8005417 14_9 1.00000 427.562 4.1477e-04 0.98639
852634 rs140185678 16_2 0.99999 45.861 4.4488e-05 7.61009
97513 rs1975584 2_118 0.99998 71.760 6.9613e-05 1.23118
580602 rs72811292 17_11 0.99998 40.044 3.8846e-05 -6.52336
279525 rs11756438 6_79 0.99997 47.694 4.6266e-05 -8.20896
117531 rs116202356 3_27 0.99993 36.106 3.5024e-05 6.08136
176218 rs1458038 4_54 0.99988 34.996 3.3945e-05 6.02778
121102 rs12330500 3_40 0.99973 519.119 5.0345e-04 0.56410
396844 rs1886296 9_73 0.99953 34.549 3.3500e-05 5.98630
39581 rs6427989 1_102 0.99932 36.397 3.5284e-05 -4.41429
653873 rs464901 22_4 0.99927 43.846 4.2503e-05 -7.05556
708945 rs574293775 5_82 0.99879 1853.693 1.7961e-03 6.24118
39582 rs12353975 1_102 0.99826 35.875 3.4741e-05 -4.30000
184120 rs7700110 4_73 0.99792 45.191 4.3748e-05 7.06667
232199 rs199992924 5_68 0.99695 1340.402 1.2963e-03 -0.63095
655632 rs133902 22_7 0.99635 31.059 3.0020e-05 6.16176
232019 rs338623 5_68 0.99536 67.127 6.4817e-05 -7.98551
414975 rs12360521 10_44 0.99534 1283.600 1.2394e-03 5.37405
696421 rs7374540 3_28 0.99390 45.861 4.4218e-05 4.77941
570915 rs876727 16_39 0.99266 48.828 4.7020e-05 -10.00000
275680 rs9496567 6_67 0.99187 26.512 2.5510e-05 5.11250
586570 rs75230966 17_27 0.99176 49.437 4.7564e-05 6.05825
183553 rs4631108 4_72 0.99154 306.031 2.9436e-04 -17.63768
40258 rs4951023 1_104 0.99062 31.135 2.9920e-05 5.59701
238444 rs6894302 5_84 0.98775 34.352 3.2916e-05 -7.29333
666039 rs2885697 1_25 0.98750 44.282 4.2420e-05 -6.27143
570920 rs60602157 16_39 0.98548 38.723 3.7019e-05 10.44156
339226 rs403894 8_19 0.97939 56.271 5.3462e-05 6.85294
650809 rs7282237 21_16 0.97823 25.002 2.3726e-05 -4.76056
529120 rs2738413 14_29 0.97821 112.527 1.0678e-04 -11.61194
570912 rs4788691 16_39 0.97479 40.133 3.7951e-05 -1.69000
329588 rs35760656 7_94 0.97466 35.328 3.3403e-05 -6.35366
470281 rs17380837 12_18 0.97380 44.428 4.1970e-05 -6.95833
366399 rs7460121 8_88 0.97258 24.195 2.2827e-05 4.75000
2727 rs284278 1_7 0.97133 35.010 3.2989e-05 -6.08571
826964 rs8011559 14_9 0.96939 435.549 4.0959e-04 5.69136
283467 rs958747 6_89 0.96881 24.377 2.2910e-05 -4.97101
556130 rs12898337 15_48 0.96439 35.443 3.3159e-05 -6.05797
279482 rs77435894 6_78 0.96424 28.808 2.6947e-05 6.11111
549931 rs745636 15_33 0.95718 25.619 2.3789e-05 -5.07407
25783 rs4839174 1_69 0.95693 33.971 3.1535e-05 5.94595
183505 rs1823291 4_72 0.95681 286.062 2.6552e-04 -19.45205
604563 rs17794590 18_24 0.95501 24.593 2.2784e-05 -4.82424
100283 rs35880620 2_125 0.95446 39.771 3.6825e-05 -6.21687
58743 rs7578482 2_16 0.95420 32.146 2.9757e-05 5.74359
738958 rs1633714 7_70 0.94997 778.224 7.1717e-04 11.75362
97488 rs11889306 2_118 0.94874 45.599 4.1967e-05 6.73913
826887 rs73241997 14_9 0.94725 276.101 2.5371e-04 7.88172
681445 rs1367220 2_105 0.94678 4303.786 3.9529e-03 7.22078
784225 rs2291437 12_17 0.94624 66.113 6.0688e-05 9.18269
32457 rs7522387 1_83 0.94609 59.861 5.4939e-05 6.63750
696586 rs7373065 3_28 0.93555 65.796 5.9714e-05 -8.06375
28495 rs906280 1_75 0.93539 59.572 5.4056e-05 7.91111
490521 rs12425471 12_69 0.93033 41.492 3.7447e-05 -5.25000
614935 rs7256735 19_3 0.92417 23.459 2.1032e-05 4.49524
279432 rs89107 6_78 0.91890 47.368 4.2225e-05 -9.56061
372071 rs1594768 9_9 0.91400 24.218 2.1473e-05 -4.69118
5627 rs10917072 1_15 0.90438 33.539 2.9425e-05 5.82353
217602 rs114414434 5_31 0.89947 26.163 2.2829e-05 -4.97183
232192 rs4073838 5_68 0.89234 1368.927 1.1850e-03 -5.95455
272609 rs371814 6_59 0.89225 1722.767 1.4912e-03 6.19118
252160 rs73724866 6_13 0.88556 94.008 8.0760e-05 -10.41414
479761 rs776211 12_43 0.88319 28.128 2.4099e-05 -6.34247
550553 rs519946 15_34 0.88197 34.471 2.9492e-05 5.92424
494561 rs6560886 12_82 0.88170 28.944 2.4757e-05 5.66667
28531 rs12128882 1_76 0.87796 32.566 2.7737e-05 1.07317
68039 rs243080 2_40 0.87491 24.167 2.0511e-05 -4.55224
467254 rs12821447 12_12 0.87169 24.081 2.0363e-05 4.51282
615414 rs73919353 19_5 0.86143 28.383 2.3719e-05 5.40764
453904 rs565449 11_55 0.85754 28.389 2.3616e-05 -5.25352
123427 rs1091584 3_45 0.85325 30.275 2.5059e-05 5.58824
244628 rs62377226 5_100 0.84223 33.879 2.7680e-05 5.84932
113948 rs73032373 3_18 0.83752 33.298 2.7054e-05 -5.91781
369034 rs72693377 8_94 0.83130 24.726 1.9940e-05 4.27624
659021 rs11705586 22_15 0.82901 26.327 2.1172e-05 4.89888
121105 rs6924 3_40 0.82773 522.730 4.1974e-04 4.21333
304278 rs145593380 7_26 0.81702 29.746 2.3576e-05 5.33333
495691 rs7321083 13_3 0.81497 24.659 1.9495e-05 4.82927SNPs with largest effect sizes
id region_tag susie_pip mu2 PVE z
681445 rs1367220 2_105 9.4678e-01 4303.8 3.9529e-03 7.22078
681435 rs4972703 2_105 1.0000e+00 4299.8 4.1712e-03 -0.78427
681446 rs1367219 2_105 2.0698e-01 4294.5 8.6229e-04 7.10390
681441 rs10168156 2_105 3.3123e-01 4292.4 1.3793e-03 7.23377
681439 rs6713018 2_105 9.6879e-02 4291.5 4.0332e-04 7.16883
681430 rs1864453 2_105 1.8765e-01 4290.0 7.8093e-04 7.20779
681422 rs2033315 2_105 1.1450e-01 4287.5 4.7625e-04 7.06494
681433 rs6707162 2_105 3.4969e-02 4279.9 1.4519e-04 7.09091
681434 rs6735680 2_105 2.4558e-02 4279.5 1.0195e-04 7.07792
681423 rs2033314 2_105 2.4327e-02 4278.4 1.0097e-04 7.15584
681425 rs28485554 2_105 8.7471e-03 4277.8 3.6299e-05 7.00000
681456 rs10803884 2_105 7.0834e-03 4217.5 2.8981e-05 7.28571
681464 rs6738901 2_105 7.7433e-03 4201.2 3.1558e-05 -7.27273
681449 rs12466643 2_105 3.1357e-04 4196.1 1.2764e-06 7.27273
681480 rs35368253 2_105 1.9984e-04 4178.4 8.1006e-07 -7.25641
681466 rs10197521 2_105 1.7633e-11 4171.6 7.1358e-14 -6.54762
681468 rs34661753 2_105 3.1944e-08 4119.4 1.2765e-10 -7.07692
681419 rs7590328 2_105 2.2724e-11 4103.4 9.0459e-14 6.78481
681417 rs6433497 2_105 0.0000e+00 3465.0 0.0000e+00 6.34568
681418 rs2115874 2_105 0.0000e+00 3462.2 0.0000e+00 6.41975
681410 rs1430185 2_105 0.0000e+00 3387.1 0.0000e+00 6.18519
681397 rs1991601 2_105 0.0000e+00 3363.1 0.0000e+00 5.95062
681395 rs6759870 2_105 0.0000e+00 2978.2 0.0000e+00 5.98734
681486 rs35215597 2_105 0.0000e+00 2793.5 0.0000e+00 -8.44156
681506 rs56181519 2_105 0.0000e+00 2703.1 0.0000e+00 -8.59740
681308 rs13032076 2_105 0.0000e+00 2402.1 0.0000e+00 -5.25000
681408 rs13024657 2_105 0.0000e+00 2366.7 0.0000e+00 -5.25806
681509 rs2358891 2_105 0.0000e+00 2265.7 0.0000e+00 -7.50000
681526 rs35808589 2_105 0.0000e+00 2030.2 0.0000e+00 -5.22989
681558 rs1376875 2_105 0.0000e+00 2019.8 0.0000e+00 -5.00000
681541 rs35444726 2_105 0.0000e+00 2016.6 0.0000e+00 -5.17241
681550 rs13420492 2_105 0.0000e+00 1989.9 0.0000e+00 -4.90805
681552 rs71417497 2_105 0.0000e+00 1980.1 0.0000e+00 -4.77273
708976 rs2040862 5_82 1.9328e-01 1961.5 3.6778e-04 12.45977
708860 rs17171711 5_82 5.0619e-02 1959.0 9.6194e-05 12.48276
708884 rs13355516 5_82 4.3981e-03 1956.7 8.3485e-06 12.37931
708835 rs9327807 5_82 2.2942e-03 1954.0 4.3488e-06 12.36782
708869 rs77915370 5_82 3.4260e-04 1952.7 6.4897e-07 12.35632
708740 rs78081438 5_82 6.6915e-04 1951.1 1.2665e-06 12.39080
708691 rs73300168 5_82 3.5658e-04 1950.8 6.7481e-07 12.29885
708817 rs11959181 5_82 9.5419e-05 1949.6 1.8047e-07 12.24138
708671 rs10076361 5_82 2.6762e-04 1949.2 5.0606e-07 12.29885
708836 rs113331339 5_82 8.8918e-05 1949.2 1.6814e-07 12.24138
708789 rs73299268 5_82 8.1699e-05 1949.1 1.5447e-07 12.24138
708892 rs148378888 5_82 1.9928e-04 1948.7 3.7672e-07 12.34483
708714 rs73299210 5_82 5.8889e-05 1946.2 1.1118e-07 12.28736
708717 rs73299219 5_82 6.2046e-05 1945.8 1.1712e-07 12.28736
708737 rs13362264 5_82 2.5455e-05 1945.4 4.8038e-08 12.26437
681335 rs2303891 2_105 0.0000e+00 1921.7 0.0000e+00 -4.18519
708899 rs10479176 5_82 6.7316e-01 1866.6 1.2189e-03 6.93182SNPs with highest PVE
id region_tag susie_pip mu2 PVE z
681435 rs4972703 2_105 1.000000 4299.78 0.00417116 -0.78427
681445 rs1367220 2_105 0.946781 4303.79 0.00395285 7.22078
708945 rs574293775 5_82 0.998792 1853.69 0.00179607 6.24118
183533 rs1906615 4_72 1.000000 1756.73 0.00170418 45.16049
272612 rs111990232 6_59 1.000000 1710.91 0.00165973 0.53927
788780 rs61937778 12_35 1.000000 1668.55 0.00161864 -1.30570
272609 rs371814 6_59 0.892251 1722.77 0.00149116 6.19118
28440 rs7536152 1_75 1.000000 1473.02 0.00142896 -6.46269
28439 rs12404927 1_75 1.000000 1437.88 0.00139486 -1.55172
681441 rs10168156 2_105 0.331231 4292.42 0.00137925 7.23377
232199 rs199992924 5_68 0.996950 1340.40 0.00129634 -0.63095
414975 rs12360521 10_44 0.995340 1283.60 0.00123940 5.37405
414968 rs76106073 10_44 1.000000 1273.72 0.00123562 0.65722
708899 rs10479176 5_82 0.673161 1866.56 0.00121891 6.93182
232192 rs4073838 5_68 0.892342 1368.93 0.00118501 -5.95455
586354 rs62056842 17_27 1.000000 1130.22 0.00109641 1.12690
788720 rs2860482 12_35 0.644935 1697.21 0.00106185 -7.10526
788775 rs7313074 12_35 0.582207 1705.11 0.00096303 -6.98684
183538 rs7440714 4_72 1.000000 992.10 0.00096242 -9.21834
681446 rs1367219 2_105 0.206980 4294.51 0.00086229 7.10390
739005 rs9770220 7_70 1.000000 835.77 0.00081077 -5.28148
681430 rs1864453 2_105 0.187650 4289.96 0.00078093 7.20779
738958 rs1633714 7_70 0.949969 778.22 0.00071717 11.75362
788778 rs4759256 12_35 0.419798 1704.63 0.00069419 -6.97368
272613 rs384318 6_59 0.379763 1721.21 0.00063410 6.10294
738995 rs10255816 7_70 0.789144 709.07 0.00054282 -9.71233
121102 rs12330500 3_40 0.999729 519.12 0.00050345 0.56410
681422 rs2033315 2_105 0.114505 4287.50 0.00047625 7.06494
272614 rs1145714 6_59 0.264787 1717.60 0.00044119 6.10294
121105 rs6924 3_40 0.827730 522.73 0.00041974 4.21333
826958 rs8005417 14_9 0.999998 427.56 0.00041477 0.98639
826964 rs8011559 14_9 0.969391 435.55 0.00040959 5.69136
681439 rs6713018 2_105 0.096879 4291.54 0.00040332 7.16883
232191 rs4235764 5_68 0.291369 1367.21 0.00038645 -5.87879
708976 rs2040862 5_82 0.193276 1961.54 0.00036778 12.45977
788715 rs7978685 12_35 0.217314 1694.86 0.00035730 -7.06579
550564 rs74022964 15_35 1.000000 342.92 0.00033266 12.57778
232194 rs4235768 5_68 0.241215 1367.36 0.00031996 -5.80303
272571 rs9444476 6_59 0.190089 1698.70 0.00031324 -6.30882
183553 rs4631108 4_72 0.991539 306.03 0.00029436 -17.63768
28533 rs34515871 1_76 1.000000 299.28 0.00029033 17.00000
272596 rs9444488 6_59 0.169741 1703.69 0.00028053 -6.26471
550561 rs140798119 15_35 1.000000 285.26 0.00027673 3.99507
183505 rs1823291 4_72 0.956815 286.06 0.00026552 -19.45205
826887 rs73241997 14_9 0.947252 276.10 0.00025371 7.88172
708944 rs191830974 5_82 0.121013 1865.78 0.00021903 6.92063
121104 rs1554125 3_40 0.389577 520.51 0.00019671 4.13333
28540 rs10908445 1_76 0.999999 193.57 0.00018778 -13.14706
272583 rs9444481 6_59 0.108496 1701.34 0.00017907 -6.25000
422177 rs60469668 10_66 1.000000 172.11 0.00016696 16.96471SNPs with largest z scores
| Version | Author | Date |
|---|---|---|
| 78023f1 | sq-96 | 2022-02-08 |
id region_tag susie_pip mu2 PVE z
183533 rs1906615 4_72 1.0000e+00 1756.73 1.7042e-03 45.160
183534 rs75725917 4_72 0.0000e+00 588.75 0.0000e+00 42.337
183532 rs1906611 4_72 0.0000e+00 526.91 0.0000e+00 40.971
183531 rs28521134 4_72 0.0000e+00 512.62 0.0000e+00 40.228
183527 rs10019689 4_72 0.0000e+00 508.50 0.0000e+00 40.110
183528 rs76013973 4_72 0.0000e+00 502.40 0.0000e+00 40.049
183530 rs12639820 4_72 0.0000e+00 499.79 0.0000e+00 40.039
183526 rs12647393 4_72 0.0000e+00 500.81 0.0000e+00 39.980
183529 rs74496596 4_72 0.0000e+00 484.73 0.0000e+00 39.757
183525 rs12647316 4_72 0.0000e+00 476.70 0.0000e+00 39.559
183524 rs4529121 4_72 0.0000e+00 480.52 0.0000e+00 39.553
183518 rs12650829 4_72 0.0000e+00 450.05 0.0000e+00 31.544
183541 rs3866831 4_72 0.0000e+00 919.46 0.0000e+00 -30.100
183540 rs6533530 4_72 0.0000e+00 904.89 0.0000e+00 -29.914
183523 rs12644107 4_72 0.0000e+00 153.07 0.0000e+00 25.989
183521 rs2723318 4_72 0.0000e+00 365.70 0.0000e+00 -25.458
183516 rs2218698 4_72 0.0000e+00 337.52 0.0000e+00 -25.096
183519 rs2197814 4_72 0.0000e+00 339.90 0.0000e+00 24.597
183517 rs1448799 4_72 0.0000e+00 339.24 0.0000e+00 24.569
183515 rs112927894 4_72 0.0000e+00 320.77 0.0000e+00 24.507
183505 rs1823291 4_72 9.5681e-01 286.06 2.6552e-04 -19.452
183509 rs2723296 4_72 4.3183e-02 278.06 1.1648e-05 -19.027
183514 rs11724067 4_72 0.0000e+00 321.19 0.0000e+00 -18.941
183508 rs2044674 4_72 2.6412e-06 253.48 6.4947e-10 18.581
183553 rs4631108 4_72 9.9154e-01 306.03 2.9436e-04 -17.638
183552 rs1906613 4_72 8.4607e-03 295.15 2.4225e-06 17.348
28533 rs34515871 1_76 1.0000e+00 299.28 2.9033e-04 17.000
422177 rs60469668 10_66 1.0000e+00 172.11 1.6696e-04 16.965
183513 rs13111704 4_72 0.0000e+00 393.83 0.0000e+00 -16.917
28536 rs12058931 1_76 1.6436e-04 221.43 3.5307e-08 16.541
183537 rs4124159 4_72 0.0000e+00 1159.18 0.0000e+00 -16.144
183535 rs1906606 4_72 0.0000e+00 1154.43 0.0000e+00 -16.027
183542 rs4032974 4_72 0.0000e+00 1146.01 0.0000e+00 -15.867
739346 rs11773845 7_70 0.0000e+00 555.73 0.0000e+00 15.731
183562 rs17513625 4_72 0.0000e+00 176.03 0.0000e+00 15.711
183539 rs10006881 4_72 0.0000e+00 1136.32 0.0000e+00 -15.688
739366 rs1997571 7_70 0.0000e+00 553.90 0.0000e+00 15.687
739329 rs3807989 7_70 0.0000e+00 551.57 0.0000e+00 15.627
422173 rs12572965 10_66 2.2738e-04 132.76 2.9285e-08 15.271
422172 rs56965730 10_66 2.3003e-04 131.79 2.9410e-08 15.212
739367 rs1997572 7_70 0.0000e+00 525.13 0.0000e+00 14.507
739223 rs2270188 7_70 0.0000e+00 711.68 0.0000e+00 14.439
739224 rs2270189 7_70 0.0000e+00 711.61 0.0000e+00 14.439
739272 rs2109514 7_70 0.0000e+00 687.78 0.0000e+00 14.424
739276 rs55883210 7_70 0.0000e+00 687.53 0.0000e+00 14.424
739239 rs10271007 7_70 0.0000e+00 707.42 0.0000e+00 14.394
739256 rs6466579 7_70 0.0000e+00 703.12 0.0000e+00 14.333
739267 rs7795510 7_70 0.0000e+00 696.72 0.0000e+00 14.227
183507 rs12642151 4_72 2.2823e-12 237.63 5.2612e-16 14.143
422175 rs7094488 10_66 1.0000e+00 110.01 1.0672e-04 14.106Gene set enrichment for genes with PIP>0.8
Welcome to enrichR
Checking connection ... Enrichr ... Connection is Live!
FlyEnrichr ... Connection is available!
WormEnrichr ... Connection is available!
YeastEnrichr ... Connection is available!
FishEnrichr ... Connection is available![1] 68Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
[1] Term Overlap Adjusted.P.value Genes
<0 rows> (or 0-length row.names)
[1] "GO_Cellular_Component_2021"
| Version | Author | Date |
|---|---|---|
| 78023f1 | sq-96 | 2022-02-08 |
Term Overlap Adjusted.P.value
1 plasma membrane raft (GO:0044853) 4/82 0.016807
Genes
1 SCARB1;STIM1;CAV1;AKAP6
[1] "GO_Molecular_Function_2021"[1] Term Overlap Adjusted.P.value Genes
<0 rows> (or 0-length row.names)POPDC3 gene(s) from the input list not found in DisGeNET CURATEDSTK11IP gene(s) from the input list not found in DisGeNET CURATEDCMTM5 gene(s) from the input list not found in DisGeNET CURATEDSP100 gene(s) from the input list not found in DisGeNET CURATEDZSWIM8 gene(s) from the input list not found in DisGeNET CURATEDRAB1A gene(s) from the input list not found in DisGeNET CURATEDNCLN gene(s) from the input list not found in DisGeNET CURATEDAES gene(s) from the input list not found in DisGeNET CURATEDJAM2 gene(s) from the input list not found in DisGeNET CURATEDFAM57A gene(s) from the input list not found in DisGeNET CURATEDMURC gene(s) from the input list not found in DisGeNET CURATEDEXOC8 gene(s) from the input list not found in DisGeNET CURATEDECE2 gene(s) from the input list not found in DisGeNET CURATEDZBTB38 gene(s) from the input list not found in DisGeNET CURATEDGIT2 gene(s) from the input list not found in DisGeNET CURATEDNBL1 gene(s) from the input list not found in DisGeNET CURATEDRP11-325L7.2 gene(s) from the input list not found in DisGeNET CURATEDC5orf47 gene(s) from the input list not found in DisGeNET CURATEDNFATC2IP gene(s) from the input list not found in DisGeNET CURATEDMARS gene(s) from the input list not found in DisGeNET CURATEDPWP1 gene(s) from the input list not found in DisGeNET CURATEDSEC23IP gene(s) from the input list not found in DisGeNET CURATEDAGAP5 gene(s) from the input list not found in DisGeNET CURATEDGLTSCR1 gene(s) from the input list not found in DisGeNET CURATEDBOK gene(s) from the input list not found in DisGeNET CURATEDGMCL1 gene(s) from the input list not found in DisGeNET CURATEDAHSA2 gene(s) from the input list not found in DisGeNET CURATEDC9orf43 gene(s) from the input list not found in DisGeNET CURATEDLINC01629 gene(s) from the input list not found in DisGeNET CURATEDRP5-890E16.5 gene(s) from the input list not found in DisGeNET CURATEDDLEU1 gene(s) from the input list not found in DisGeNET CURATEDLIN54 gene(s) from the input list not found in DisGeNET CURATEDPAFAH1B2 gene(s) from the input list not found in DisGeNET CURATED Description FDR Ratio BgRatio
135 Paroxysmal atrial fibrillation 3.4616e-13 13/35 156/9703
257 Persistent atrial fibrillation 3.4616e-13 13/35 156/9703
279 familial atrial fibrillation 3.4616e-13 13/35 156/9703
6 Atrial Fibrillation 3.6249e-13 13/35 160/9703
7 Auriculo-Ventricular Dissociation 4.0788e-03 2/35 4/9703
48 Heart Block 4.0788e-03 2/35 4/9703
185 Thyroid Agenesis 5.8136e-03 2/35 5/9703
41 Follicular cyst 2.5974e-02 1/35 1/9703
49 Cardiomegaly 2.5974e-02 3/35 82/9703
67 Malaria 2.5974e-02 2/35 20/9703******************************************
* *
* Welcome to WebGestaltR ! *
* *
******************************************
| Version | Author | Date |
|---|---|---|
| 78023f1 | sq-96 | 2022-02-08 |
Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...
description size overlap FDR database
1 Atrial Fibrillation 52 6 0.0026153 disease_GLAD4U
2 Arrhythmias, Cardiac 89 6 0.0236249 disease_GLAD4U
3 Isaacs Syndrome 55 5 0.0236249 disease_GLAD4U
userId
1 PRRX1;SCN10A;NKX2-5;CAV1;SYNPO2L;KCNJ5
2 PRRX1;SCN10A;NKX2-5;CAV1;SYNPO2L;KCNJ5
3 SCN10A;GNB4;NKX2-5;CCND2;KLF12PIP Manhattan Plot
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──✔ tidyr 1.1.4 ✔ dplyr 1.0.7
✔ readr 2.1.1 ✔ stringr 1.4.0
✔ purrr 0.3.4 ✔ forcats 0.5.1── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ tidyr::extract() masks disgenet2r::extract()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()Warning: ggrepel: 21 unlabeled data points (too many overlaps). Consider
increasing max.overlaps
Locus Plots - 12_75
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.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] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[5] readr_2.1.1 tidyr_1.1.4 tidyverse_1.3.1 tibble_3.1.6
[9] WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0 cowplot_1.0.0
[13] ggplot2_3.3.5 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.2 lubridate_1.8.0 bit64_4.0.5 doParallel_1.0.16
[5] httr_1.4.2 rprojroot_2.0.2 tools_3.6.1 backports_1.4.1
[9] doRNG_1.8.2 utf8_1.2.2 R6_2.5.1 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.3 ggrastr_1.0.1
[17] tidyselect_1.1.1 bit_4.0.4 curl_4.3.2 compiler_3.6.1
[21] git2r_0.26.1 cli_3.1.0 rvest_1.0.2 Cairo_1.5-12.2
[25] xml2_1.3.3 labeling_0.4.2 scales_1.1.1 apcluster_1.4.8
[29] digest_0.6.29 rmarkdown_2.11 svglite_1.2.2 pkgconfig_2.0.3
[33] htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 highr_0.9
[37] rlang_0.4.12 readxl_1.3.1 rstudioapi_0.13 RSQLite_2.2.8
[41] jquerylib_0.1.4 farver_2.1.0 generics_0.1.1 jsonlite_1.7.2
[45] vroom_1.5.7 magrittr_2.0.1 Matrix_1.2-18 ggbeeswarm_0.6.0
[49] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0 gdtools_0.1.9
[53] lifecycle_1.0.1 stringi_1.7.6 whisker_0.3-2 yaml_2.2.1
[57] plyr_1.8.6 grid_3.6.1 blob_1.2.2 ggrepel_0.9.1
[61] parallel_3.6.1 promises_1.0.1 crayon_1.4.2 lattice_0.20-38
[65] haven_2.4.3 hms_1.1.1 knitr_1.36 pillar_1.6.4
[69] igraph_1.2.10 rjson_0.2.20 rngtools_1.5.2 reshape2_1.4.4
[73] codetools_0.2-16 reprex_2.0.1 glue_1.5.1 evaluate_0.14
[77] data.table_1.14.2 modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0
[81] httpuv_1.5.1 foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0
[85] assertthat_0.2.1 cachem_1.0.6 xfun_0.29 broom_0.7.10
[89] later_0.8.0 iterators_1.0.13 beeswarm_0.2.3 memoise_2.0.1
[93] ellipsis_0.3.2