********************************************************************* * LD Score Regression (LDSC) * Version 1.0.0 * (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane * Broad Institute of MIT and Harvard / MIT Department of Mathematics * GNU General Public License v3 ********************************************************************* Call: ./ldsc.py \ --print-snps hapmap3_snps/hm.9.snp \ --ld-wind-cm 1.0 \ --out 1000G_Phase3_baseline_v1.1_rerun/baseline.9 \ --bfile 1000G_EUR_Phase3_plink/1000G.EUR.QC.9 \ --annot 1000G_Phase3_baseline_v1.1/baseline.9.annot.gz \ --l2 Beginning analysis at Tue Oct 17 16:41:15 2017 Read list of 438106 SNPs from 1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bim Read 53 annotations for 438106 SNPs from 1000G_Phase3_baseline_v1.1/baseline.9.annot.gz Read list of 489 individuals from 1000G_EUR_Phase3_plink/1000G.EUR.QC.9.fam Reading genotypes from 1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bed Estimating LD Score. Reading list of 63706 SNPs for which to print LD Scores from hapmap3_snps/hm.9.snp After merging with --print-snps, LD Scores for 55885 SNPs will be printed. Writing LD Scores for 55885 SNPs to 1000G_Phase3_baseline_v1.1_rerun/baseline.9.l2.ldscore.gz Summary of LD Scores in 1000G_Phase3_baseline_v1.1_rerun/baseline.9.l2.ldscore.gz MAF baseL2 Coding_UCSC.bedL2 Coding_UCSC.extend.500.bedL2 Conserved_LindbladToh.bedL2 Conserved_LindbladToh.extend.500.bedL2 CTCF_Hoffman.bedL2 CTCF_Hoffman.extend.500.bedL2 DGF_ENCODE.bedL2 DGF_ENCODE.extend.500.bedL2 DHS_peaks_Trynka.bedL2 DHS_Trynka.bedL2 DHS_Trynka.extend.500.bedL2 Enhancer_Andersson.bedL2 Enhancer_Andersson.extend.500.bedL2 Enhancer_Hoffman.bedL2 Enhancer_Hoffman.extend.500.bedL2 FetalDHS_Trynka.bedL2 FetalDHS_Trynka.extend.500.bedL2 H3K27ac_Hnisz.bedL2 H3K27ac_Hnisz.extend.500.bedL2 H3K27ac_PGC2.bedL2 H3K27ac_PGC2.extend.500.bedL2 H3K4me1_peaks_Trynka.bedL2 H3K4me1_Trynka.bedL2 H3K4me1_Trynka.extend.500.bedL2 H3K4me3_peaks_Trynka.bedL2 H3K4me3_Trynka.bedL2 H3K4me3_Trynka.extend.500.bedL2 H3K9ac_peaks_Trynka.bedL2 H3K9ac_Trynka.bedL2 H3K9ac_Trynka.extend.500.bedL2 Intron_UCSC.bedL2 Intron_UCSC.extend.500.bedL2 PromoterFlanking_Hoffman.bedL2 PromoterFlanking_Hoffman.extend.500.bedL2 Promoter_UCSC.bedL2 \ mean 0.2343 105.6942 1.4493 6.9356 2.9229 34.7961 2.0992 6.3104 13.6218 54.8556 11.5210 17.3266 51.3545 0.3758 1.6716 3.6495 7.9650 8.5888 28.9097 40.5423 43.7176 27.6841 34.4084 17.9353 44.3446 63.1898 4.0497 12.8578 25.0139 4.1403 13.1361 23.9600 46.0793 46.9830 0.8547 3.2089 4.9439 std 0.1436 85.8890 2.6642 11.3943 3.2614 27.8539 2.2498 6.2481 11.9661 42.7876 9.4345 13.6757 37.8224 0.7223 2.6268 5.5728 11.1364 7.3666 22.5428 41.5480 43.1662 29.4720 35.0537 17.7243 38.7886 50.7939 4.8882 14.4489 24.2892 6.0785 17.2389 28.0391 60.5785 61.2650 1.4496 4.6951 8.0303 min 0.0051 -1.0385 -0.1681 -0.5996 -0.1348 -0.9774 -0.1771 -0.3932 -0.2687 -0.7756 -0.4099 -0.3641 -0.2641 -0.0552 -0.1487 -0.3554 -0.4755 -0.2778 -0.5365 -2.4898 -2.6580 -1.3148 -1.4909 -0.6736 -0.7167 -0.8696 -0.3952 -0.9430 -1.6650 -0.3122 -1.0125 -1.2739 -3.1406 -3.0757 -0.0988 -0.2051 -0.4249 25% 0.1084 48.8484 0.0389 0.2768 0.9391 16.0931 0.5178 1.9664 5.5153 25.5540 5.0848 8.0077 25.1894 0.0115 0.1412 0.3388 0.9953 3.5573 13.4427 11.7958 13.9708 7.8472 10.5398 6.3731 18.1355 28.8131 1.0366 3.8144 9.0940 0.6073 2.4307 5.8560 4.0147 4.1684 0.0425 0.3097 0.2886 50% 0.2239 81.8714 0.3435 2.1560 2.0819 27.5048 1.3524 4.3475 10.1343 42.8537 8.9101 13.5539 40.8269 0.0849 0.6889 1.5021 3.6502 6.5466 22.7857 27.1905 30.2452 17.9667 23.1571 12.3632 32.5854 48.3988 2.3777 7.9597 17.2955 1.9801 6.9764 14.3159 25.1760 25.9756 0.2241 1.3197 1.7210 75% 0.3558 132.8186 1.6482 8.7521 3.8584 45.6683 2.8568 8.4868 17.7541 71.7738 15.0613 22.7409 67.2687 0.3849 2.1160 4.5731 10.3071 11.1027 37.5542 54.7132 58.5248 36.8284 45.8822 22.7623 57.5246 81.4661 5.0815 16.2193 31.9789 4.9581 16.5783 31.3948 65.4067 66.6570 1.0427 4.1161 6.3021 max 0.5000 693.7645 40.9598 122.3905 51.7421 265.7667 17.4518 43.4642 85.7759 301.8028 75.4034 105.5465 293.4876 8.0650 29.4886 71.4839 108.8581 56.1805 173.0080 284.3637 291.5474 236.2724 271.6907 149.1778 281.7306 383.0187 51.4601 136.7535 216.9391 66.9998 158.2973 210.9322 533.4846 535.4412 14.7248 49.0362 90.1105 Promoter_UCSC.extend.500.bedL2 Repressed_Hoffman.bedL2 Repressed_Hoffman.extend.500.bedL2 SuperEnhancer_Hnisz.bedL2 SuperEnhancer_Hnisz.extend.500.bedL2 TFBS_ENCODE.bedL2 TFBS_ENCODE.extend.500.bedL2 Transcribed_Hoffman.bedL2 Transcribed_Hoffman.extend.500.bedL2 TSS_Hoffman.bedL2 TSS_Hoffman.extend.500.bedL2 UTR_3_UCSC.bedL2 UTR_3_UCSC.extend.500.bedL2 UTR_5_UCSC.bedL2 UTR_5_UCSC.extend.500.bedL2 WeakEnhancer_Hoffman.bedL2 WeakEnhancer_Hoffman.extend.500.bedL2 mean 6.0738 47.8794 74.7816 17.6747 17.9814 12.8544 33.8166 36.6349 77.0133 1.6668 3.1127 1.1490 2.7515 0.6194 3.0370 1.7269 7.6154 std 9.7939 52.4884 76.5154 29.4508 29.7244 12.4082 28.5522 43.6080 69.5814 3.2447 5.4340 2.1756 5.0663 1.4302 5.5287 2.4062 9.4261 min -0.4281 -2.2071 -2.8497 -1.5642 -1.5882 -0.3086 -0.7865 -1.6062 -1.6080 -0.2570 -0.3082 -0.1292 -0.3622 -0.1397 -0.2974 -0.1534 -0.5360 25% 0.3618 14.7409 26.5318 0.3876 0.4073 4.5627 14.1157 10.0481 31.2171 0.0445 0.1281 0.0253 0.0881 0.0085 0.1280 0.2223 1.5409 50% 2.1639 32.9918 53.9807 4.1157 4.3063 8.8857 25.2274 20.6143 56.6356 0.3236 0.8450 0.2377 0.6858 0.0856 0.8405 0.8082 4.2292 75% 7.8112 62.0225 96.6466 23.6286 24.1427 16.5662 44.6608 44.7568 97.2938 1.7603 3.6715 1.2439 3.1866 0.4988 3.2729 2.1790 9.7668 max 111.2501 505.8116 692.8826 263.4521 264.5251 114.7155 206.1799 338.0531 523.2192 37.4558 59.9526 39.8106 62.6158 21.0957 51.2877 22.6747 71.6451 MAF/LD Score Correlation Matrix MAF baseL2 Coding_UCSC.bedL2 Coding_UCSC.extend.500.bedL2 Conserved_LindbladToh.bedL2 Conserved_LindbladToh.extend.500.bedL2 CTCF_Hoffman.bedL2 CTCF_Hoffman.extend.500.bedL2 DGF_ENCODE.bedL2 DGF_ENCODE.extend.500.bedL2 DHS_peaks_Trynka.bedL2 DHS_Trynka.bedL2 DHS_Trynka.extend.500.bedL2 Enhancer_Andersson.bedL2 Enhancer_Andersson.extend.500.bedL2 Enhancer_Hoffman.bedL2 Enhancer_Hoffman.extend.500.bedL2 FetalDHS_Trynka.bedL2 FetalDHS_Trynka.extend.500.bedL2 H3K27ac_Hnisz.bedL2 H3K27ac_Hnisz.extend.500.bedL2 H3K27ac_PGC2.bedL2 H3K27ac_PGC2.extend.500.bedL2 H3K4me1_peaks_Trynka.bedL2 H3K4me1_Trynka.bedL2 H3K4me1_Trynka.extend.500.bedL2 H3K4me3_peaks_Trynka.bedL2 H3K4me3_Trynka.bedL2 H3K4me3_Trynka.extend.500.bedL2 H3K9ac_peaks_Trynka.bedL2 H3K9ac_Trynka.bedL2 H3K9ac_Trynka.extend.500.bedL2 Intron_UCSC.bedL2 Intron_UCSC.extend.500.bedL2 PromoterFlanking_Hoffman.bedL2 PromoterFlanking_Hoffman.extend.500.bedL2 \ MAF 1.0000 0.1718 0.0542 0.0497 0.1041 0.1675 0.1367 0.1532 0.1536 0.1777 0.1805 0.1810 0.1875 0.0677 0.0940 0.0740 0.0802 0.1657 0.1796 0.1243 0.1295 0.1070 0.1161 0.1255 0.1422 0.1618 0.0776 0.0937 0.1158 0.0723 0.0798 0.0904 0.0838 0.0841 0.0564 0.0782 baseL2 0.1718 1.0000 0.3320 0.3931 0.5558 0.7686 0.5114 0.5905 0.6588 0.8094 0.7109 0.7403 0.8444 0.2068 0.2651 0.3161 0.3669 0.6388 0.7285 0.4967 0.5268 0.5165 0.5450 0.5548 0.6468 0.7553 0.4956 0.5295 0.6238 0.3774 0.4147 0.4656 0.5874 0.5889 0.4470 0.5018 Coding_UCSC.bedL2 0.0542 0.3320 1.0000 0.8519 0.2382 0.4240 0.4923 0.5438 0.5572 0.5164 0.4734 0.4654 0.4610 0.2288 0.2487 0.4728 0.5130 0.4681 0.4497 0.5014 0.5091 0.5181 0.5265 0.5272 0.5563 0.5291 0.5952 0.6228 0.5995 0.5912 0.6237 0.6385 0.4400 0.4560 0.4807 0.5648 Coding_UCSC.extend.500.bedL2 0.0497 0.3931 0.8519 1.0000 0.2812 0.5317 0.5559 0.6238 0.6683 0.6237 0.5701 0.5623 0.5622 0.2523 0.2941 0.5491 0.5991 0.5541 0.5439 0.6227 0.6320 0.6318 0.6434 0.6364 0.6808 0.6493 0.6759 0.7060 0.6890 0.6862 0.7187 0.7460 0.5770 0.5927 0.5886 0.6541 Conserved_LindbladToh.bedL2 0.1041 0.5558 0.2382 0.2812 1.0000 0.8148 0.3492 0.3842 0.5129 0.5771 0.5904 0.6098 0.6188 0.1383 0.1836 0.3150 0.3409 0.5440 0.5707 0.4108 0.4283 0.4209 0.4404 0.4829 0.5333 0.5788 0.3759 0.3925 0.4395 0.3426 0.3601 0.3967 0.5051 0.5049 0.4085 0.4586 Conserved_LindbladToh.extend.500.bedL2 0.1675 0.7686 0.4240 0.5317 0.8148 1.0000 0.5664 0.6227 0.7504 0.8298 0.8137 0.8340 0.8621 0.2897 0.3709 0.4898 0.5334 0.7598 0.8074 0.6584 0.6798 0.6731 0.6951 0.7133 0.7841 0.8307 0.5875 0.6148 0.6752 0.5455 0.5796 0.6266 0.6950 0.6975 0.5545 0.6134 CTCF_Hoffman.bedL2 0.1367 0.5114 0.4923 0.5559 0.3492 0.5664 1.0000 0.9223 0.7328 0.7173 0.7005 0.6966 0.6796 0.3302 0.4011 0.5339 0.5862 0.6828 0.6791 0.6626 0.6744 0.6612 0.6725 0.6850 0.7039 0.7003 0.6342 0.6497 0.6717 0.6383 0.6612 0.6919 0.5335 0.5403 0.4877 0.5800 CTCF_Hoffman.extend.500.bedL2 0.1532 0.5905 0.5438 0.6238 0.3842 0.6227 0.9223 1.0000 0.8027 0.7955 0.7623 0.7596 0.7535 0.3665 0.4375 0.5923 0.6457 0.7412 0.7495 0.7263 0.7395 0.7203 0.7338 0.7494 0.7725 0.7725 0.6986 0.7197 0.7494 0.7069 0.7305 0.7636 0.5812 0.5894 0.5501 0.6447 DGF_ENCODE.bedL2 0.1536 0.6588 0.5572 0.6683 0.5129 0.7504 0.7328 0.8027 1.0000 0.9504 0.9470 0.9444 0.9131 0.4920 0.5883 0.7553 0.7990 0.9108 0.9131 0.9035 0.9146 0.9113 0.9241 0.9441 0.9569 0.9398 0.8512 0.8792 0.9160 0.8220 0.8616 0.8984 0.7159 0.7225 0.6591 0.7471 DGF_ENCODE.extend.500.bedL2 0.1777 0.8094 0.5164 0.6237 0.5771 0.8298 0.7173 0.7955 0.9504 1.0000 0.9443 0.9544 0.9766 0.4185 0.5188 0.6494 0.7067 0.8883 0.9316 0.8544 0.8747 0.8573 0.8808 0.8916 0.9455 0.9755 0.7735 0.8080 0.8784 0.7143 0.7660 0.8204 0.7517 0.7565 0.6493 0.7288 DHS_peaks_Trynka.bedL2 0.1805 0.7109 0.4734 0.5701 0.5904 0.8137 0.7005 0.7623 0.9470 0.9443 1.0000 0.9866 0.9491 0.4600 0.5609 0.6791 0.7223 0.9589 0.9558 0.8660 0.8802 0.8706 0.8867 0.9118 0.9369 0.9397 0.7849 0.8065 0.8636 0.7414 0.7833 0.8250 0.7136 0.7175 0.6063 0.6899 DHS_Trynka.bedL2 0.1810 0.7403 0.4654 0.5623 0.6098 0.8340 0.6966 0.7596 0.9444 0.9544 0.9866 1.0000 0.9656 0.4538 0.5569 0.6736 0.7151 0.9527 0.9594 0.8582 0.8737 0.8680 0.8847 0.9086 0.9374 0.9478 0.7734 0.7975 0.8601 0.7294 0.7698 0.8137 0.7204 0.7241 0.5971 0.6803 DHS_Trynka.extend.500.bedL2 0.1875 0.8444 0.4610 0.5622 0.6188 0.8621 0.6796 0.7535 0.9131 0.9766 0.9491 0.9656 1.0000 0.4041 0.5032 0.6121 0.6646 0.8979 0.9531 0.8178 0.8395 0.8217 0.8453 0.8658 0.9225 0.9628 0.7303 0.7651 0.8451 0.6647 0.7138 0.7685 0.7355 0.7388 0.6041 0.6790 Enhancer_Andersson.bedL2 0.0677 0.2068 0.2288 0.2523 0.1383 0.2897 0.3302 0.3665 0.4920 0.4185 0.4600 0.4538 0.4041 1.0000 0.8599 0.4899 0.4714 0.4845 0.4565 0.5169 0.5090 0.5403 0.5226 0.5169 0.4784 0.4231 0.4908 0.4959 0.4793 0.4792 0.4965 0.4838 0.2721 0.2752 0.2985 0.3260 Enhancer_Andersson.extend.500.bedL2 0.0940 0.2651 0.2487 0.2941 0.1836 0.3709 0.4011 0.4375 0.5883 0.5188 0.5609 0.5569 0.5032 0.8599 1.0000 0.5721 0.5620 0.5844 0.5652 0.6213 0.6138 0.6484 0.6311 0.6228 0.5787 0.5214 0.5683 0.5799 0.5749 0.5630 0.5819 0.5728 0.3462 0.3489 0.3531 0.3899 Enhancer_Hoffman.bedL2 0.0740 0.3161 0.4728 0.5491 0.3150 0.4898 0.5339 0.5923 0.7553 0.6494 0.6791 0.6736 0.6121 0.4899 0.5721 1.0000 0.9700 0.7079 0.6828 0.7679 0.7615 0.8007 0.7828 0.8066 0.7415 0.6655 0.7813 0.7788 0.7618 0.7831 0.7808 0.7833 0.5121 0.5188 0.5421 0.6345 Enhancer_Hoffman.extend.500.bedL2 0.0802 0.3669 0.5130 0.5991 0.3409 0.5334 0.5862 0.6457 0.7990 0.7067 0.7223 0.7151 0.6646 0.4714 0.5620 0.9700 1.0000 0.7396 0.7210 0.8125 0.8099 0.8429 0.8308 0.8461 0.7932 0.7256 0.8121 0.8204 0.8096 0.8099 0.8154 0.8270 0.5667 0.5740 0.6065 0.7100 FetalDHS_Trynka.bedL2 0.1657 0.6388 0.4681 0.5541 0.5440 0.7598 0.6828 0.7412 0.9108 0.8883 0.9589 0.9527 0.8979 0.4845 0.5844 0.7079 0.7396 1.0000 0.9614 0.8616 0.8702 0.8679 0.8774 0.9086 0.9116 0.8941 0.7954 0.8069 0.8496 0.7664 0.7935 0.8245 0.6709 0.6752 0.5862 0.6719 FetalDHS_Trynka.extend.500.bedL2 0.1796 0.7285 0.4497 0.5439 0.5707 0.8074 0.6791 0.7495 0.9131 0.9316 0.9558 0.9594 0.9531 0.4565 0.5652 0.6828 0.7210 0.9614 1.0000 0.8610 0.8744 0.8630 0.8771 0.9061 0.9293 0.9324 0.7648 0.7900 0.8547 0.7281 0.7655 0.8082 0.7034 0.7068 0.5909 0.6684 H3K27ac_Hnisz.bedL2 0.1243 0.4967 0.5014 0.6227 0.4108 0.6584 0.6626 0.7263 0.9035 0.8544 0.8660 0.8582 0.8178 0.5169 0.6213 0.7679 0.8125 0.8616 0.8610 1.0000 0.9978 0.9518 0.9586 0.9379 0.9352 0.8834 0.8144 0.8432 0.8737 0.8135 0.8659 0.9035 0.6676 0.6738 0.6353 0.7183 H3K27ac_Hnisz.extend.500.bedL2 0.1295 0.5268 0.5091 0.6320 0.4283 0.6798 0.6744 0.7395 0.9146 0.8747 0.8802 0.8737 0.8395 0.5090 0.6138 0.7615 0.8099 0.8702 0.8744 0.9978 1.0000 0.9531 0.9626 0.9426 0.9470 0.9028 0.8168 0.8468 0.8818 0.8098 0.8637 0.9050 0.6825 0.6887 0.6488 0.7309 H3K27ac_PGC2.bedL2 0.1070 0.5165 0.5181 0.6318 0.4209 0.6731 0.6612 0.7203 0.9113 0.8573 0.8706 0.8680 0.8217 0.5403 0.6484 0.8007 0.8429 0.8679 0.8630 0.9518 0.9531 1.0000 0.9954 0.9459 0.9392 0.8841 0.8433 0.8688 0.8937 0.8444 0.8872 0.9173 0.6920 0.6980 0.6502 0.7318 H3K27ac_PGC2.extend.500.bedL2 0.1161 0.5450 0.5265 0.6434 0.4404 0.6951 0.6725 0.7338 0.9241 0.8808 0.8867 0.8847 0.8453 0.5226 0.6311 0.7828 0.8308 0.8774 0.8771 0.9586 0.9626 0.9954 1.0000 0.9502 0.9544 0.9084 0.8385 0.8674 0.8999 0.8313 0.8803 0.9177 0.7117 0.7177 0.6618 0.7442 H3K4me1_peaks_Trynka.bedL2 0.1255 0.5548 0.5272 0.6364 0.4829 0.7133 0.6850 0.7494 0.9441 0.8916 0.9118 0.9086 0.8658 0.5169 0.6228 0.8066 0.8461 0.9086 0.9061 0.9379 0.9426 0.9459 0.9502 1.0000 0.9665 0.9196 0.8696 0.8883 0.9142 0.8732 0.8991 0.9266 0.7115 0.7172 0.6779 0.7494 H3K4me1_Trynka.bedL2 0.1422 0.6468 0.5563 0.6808 0.5333 0.7841 0.7039 0.7725 0.9569 0.9455 0.9369 0.9374 0.9225 0.4784 0.5787 0.7415 0.7932 0.9116 0.9293 0.9352 0.9470 0.9392 0.9544 0.9665 1.0000 0.9780 0.8363 0.8686 0.9166 0.8109 0.8624 0.9115 0.7612 0.7674 0.6925 0.7656 H3K4me1_Trynka.extend.500.bedL2 0.1618 0.7553 0.5291 0.6493 0.5788 0.8307 0.7003 0.7725 0.9398 0.9755 0.9397 0.9478 0.9628 0.4231 0.5214 0.6655 0.7256 0.8941 0.9324 0.8834 0.9028 0.8841 0.9084 0.9196 0.9780 1.0000 0.7852 0.8211 0.8879 0.7309 0.7874 0.8476 0.7898 0.7947 0.6796 0.7528 H3K4me3_peaks_Trynka.bedL2 0.0776 0.4956 0.5952 0.6759 0.3759 0.5875 0.6342 0.6986 0.8512 0.7735 0.7849 0.7734 0.7303 0.4908 0.5683 0.7813 0.8121 0.7954 0.7648 0.8144 0.8168 0.8433 0.8385 0.8696 0.8363 0.7852 1.0000 0.9550 0.9270 0.8849 0.8934 0.8794 0.5979 0.6082 0.6548 0.7533 H3K4me3_Trynka.bedL2 0.0937 0.5295 0.6228 0.7060 0.3925 0.6148 0.6497 0.7197 0.8792 0.8080 0.8065 0.7975 0.7651 0.4959 0.5799 0.7788 0.8204 0.8069 0.7900 0.8432 0.8468 0.8688 0.8674 0.8883 0.8686 0.8211 0.9550 1.0000 0.9738 0.8821 0.9114 0.9059 0.6220 0.6327 0.6640 0.7665 H3K4me3_Trynka.extend.500.bedL2 0.1158 0.6238 0.5995 0.6890 0.4395 0.6752 0.6717 0.7494 0.9160 0.8784 0.8636 0.8601 0.8451 0.4793 0.5749 0.7618 0.8096 0.8496 0.8547 0.8737 0.8818 0.8937 0.8999 0.9142 0.9166 0.8879 0.9270 0.9738 1.0000 0.8554 0.8955 0.9123 0.6779 0.6869 0.6664 0.7680 H3K9ac_peaks_Trynka.bedL2 0.0723 0.3774 0.5912 0.6862 0.3426 0.5455 0.6383 0.7069 0.8220 0.7143 0.7414 0.7294 0.6647 0.4792 0.5630 0.7831 0.8099 0.7664 0.7281 0.8135 0.8098 0.8444 0.8313 0.8732 0.8109 0.7309 0.8849 0.8821 0.8554 1.0000 0.9661 0.9387 0.5618 0.5719 0.6035 0.6974 H3K9ac_Trynka.bedL2 0.0798 0.4147 0.6237 0.7187 0.3601 0.5796 0.6612 0.7305 0.8616 0.7660 0.7833 0.7698 0.7138 0.4965 0.5819 0.7808 0.8154 0.7935 0.7655 0.8659 0.8637 0.8872 0.8803 0.8991 0.8624 0.7874 0.8934 0.9114 0.8955 0.9661 1.0000 0.9811 0.5983 0.6086 0.6133 0.7139 H3K9ac_Trynka.extend.500.bedL2 0.0904 0.4656 0.6385 0.7460 0.3967 0.6266 0.6919 0.7636 0.8984 0.8204 0.8250 0.8137 0.7685 0.4838 0.5728 0.7833 0.8270 0.8245 0.8082 0.9035 0.9050 0.9173 0.9177 0.9266 0.9115 0.8476 0.8794 0.9059 0.9123 0.9387 0.9811 1.0000 0.6541 0.6639 0.6514 0.7489 Intron_UCSC.bedL2 0.0838 0.5874 0.4400 0.5770 0.5051 0.6950 0.5335 0.5812 0.7159 0.7517 0.7136 0.7204 0.7355 0.2721 0.3462 0.5121 0.5667 0.6709 0.7034 0.6676 0.6825 0.6920 0.7117 0.7115 0.7612 0.7898 0.5979 0.6220 0.6779 0.5618 0.5983 0.6541 1.0000 0.9997 0.5454 0.5996 Intron_UCSC.extend.500.bedL2 0.0841 0.5889 0.4560 0.5927 0.5049 0.6975 0.5403 0.5894 0.7225 0.7565 0.7175 0.7241 0.7388 0.2752 0.3489 0.5188 0.5740 0.6752 0.7068 0.6738 0.6887 0.6980 0.7177 0.7172 0.7674 0.7947 0.6082 0.6327 0.6869 0.5719 0.6086 0.6639 0.9997 1.0000 0.5524 0.6083 PromoterFlanking_Hoffman.bedL2 0.0564 0.4470 0.4807 0.5886 0.4085 0.5545 0.4877 0.5501 0.6591 0.6493 0.6063 0.5971 0.6041 0.2985 0.3531 0.5421 0.6065 0.5862 0.5909 0.6353 0.6488 0.6502 0.6618 0.6779 0.6925 0.6796 0.6548 0.6640 0.6664 0.6035 0.6133 0.6514 0.5454 0.5524 1.0000 0.9013 PromoterFlanking_Hoffman.extend.500.bedL2 0.0782 0.5018 0.5648 0.6541 0.4586 0.6134 0.5800 0.6447 0.7471 0.7288 0.6899 0.6803 0.6790 0.3260 0.3899 0.6345 0.7100 0.6719 0.6684 0.7183 0.7309 0.7318 0.7442 0.7494 0.7656 0.7528 0.7533 0.7665 0.7680 0.6974 0.7139 0.7489 0.5996 0.6083 0.9013 1.0000 Promoter_UCSC.bedL2 0.0543 0.4343 0.7386 0.7786 0.2557 0.4654 0.5587 0.6445 0.6651 0.6215 0.5702 0.5602 0.5558 0.2966 0.3369 0.5524 0.6085 0.5575 0.5498 0.6181 0.6265 0.6242 0.6320 0.6402 0.6614 0.6348 0.7145 0.7355 0.7140 0.6868 0.7116 0.7240 0.4795 0.4936 0.5956 0.6723 Promoter_UCSC.extend.500.bedL2 0.0584 0.4405 0.7411 0.7795 0.2591 0.4661 0.5639 0.6496 0.6656 0.6255 0.5695 0.5609 0.5586 0.2923 0.3311 0.5449 0.6017 0.5558 0.5502 0.6184 0.6275 0.6231 0.6319 0.6399 0.6632 0.6388 0.7057 0.7287 0.7100 0.6829 0.7082 0.7231 0.4891 0.5030 0.5985 0.6712 Repressed_Hoffman.bedL2 0.1528 0.7969 -0.0432 -0.0755 0.3321 0.4393 0.1478 0.1960 0.1793 0.3760 0.2950 0.3288 0.4503 -0.0107 0.0059 -0.1619 -0.1531 0.2339 0.3301 0.0086 0.0351 0.0282 0.0512 0.0515 0.1529 0.2924 0.0222 0.0447 0.1430 -0.0952 -0.0727 -0.0457 0.1634 0.1597 0.0072 0.0168 Repressed_Hoffman.extend.500.bedL2 0.1597 0.8498 0.0110 -0.0137 0.3841 0.5077 0.2149 0.2665 0.2588 0.4581 0.3719 0.4058 0.5279 0.0220 0.0440 -0.1043 -0.0844 0.3030 0.4007 0.0855 0.1138 0.1057 0.1313 0.1314 0.2363 0.3781 0.0975 0.1172 0.2200 -0.0303 -0.0016 0.0303 0.2599 0.2563 0.0750 0.0943 SuperEnhancer_Hnisz.bedL2 0.0738 0.2928 0.3543 0.4472 0.2032 0.4345 0.5141 0.5653 0.7142 0.6216 0.6641 0.6554 0.5829 0.5722 0.6638 0.7097 0.7104 0.7010 0.6720 0.8294 0.8102 0.8380 0.8149 0.7880 0.7327 0.6400 0.7040 0.7128 0.7130 0.7604 0.7806 0.7770 0.5012 0.5050 0.4277 0.4919 SuperEnhancer_Hnisz.extend.500.bedL2 0.0746 0.2970 0.3575 0.4509 0.2067 0.4388 0.5181 0.5693 0.7179 0.6262 0.6680 0.6593 0.5872 0.5725 0.6644 0.7106 0.7118 0.7038 0.6752 0.8327 0.8137 0.8410 0.8183 0.7907 0.7367 0.6447 0.7063 0.7156 0.7164 0.7620 0.7831 0.7801 0.5054 0.5092 0.4306 0.4958 TFBS_ENCODE.bedL2 0.1339 0.6043 0.5964 0.6980 0.4711 0.7110 0.7397 0.8080 0.9380 0.8910 0.8871 0.8851 0.8560 0.4833 0.5805 0.8153 0.8580 0.8696 0.8694 0.8795 0.8883 0.8959 0.9011 0.9150 0.9172 0.8889 0.8781 0.8990 0.9114 0.8473 0.8764 0.8981 0.6608 0.6700 0.6579 0.7610 TFBS_ENCODE.extend.500.bedL2 0.1570 0.7330 0.5600 0.6668 0.5278 0.7821 0.7460 0.8289 0.9521 0.9593 0.9292 0.9343 0.9370 0.4556 0.5563 0.7416 0.7954 0.8938 0.9222 0.8826 0.8977 0.8921 0.9060 0.9178 0.9461 0.9482 0.8374 0.8670 0.9123 0.7914 0.8324 0.8723 0.7131 0.7202 0.6685 0.7568 Transcribed_Hoffman.bedL2 0.0799 0.7267 0.5512 0.7001 0.5208 0.7233 0.5676 0.6464 0.7905 0.8280 0.7460 0.7619 0.8117 0.2800 0.3445 0.6286 0.6982 0.6980 0.7470 0.7122 0.7327 0.7287 0.7494 0.7686 0.8066 0.8342 0.7009 0.7364 0.7823 0.6498 0.6775 0.7306 0.7377 0.7435 0.6818 0.7413 Transcribed_Hoffman.extend.500.bedL2 0.1420 0.9652 0.3581 0.4427 0.5725 0.7698 0.4796 0.5619 0.6588 0.7961 0.6986 0.7291 0.8325 0.1909 0.2482 0.3629 0.4191 0.6318 0.7190 0.5107 0.5391 0.5370 0.5630 0.5759 0.6549 0.7537 0.5190 0.5533 0.6393 0.4148 0.4459 0.4948 0.6336 0.6353 0.4825 0.5368 TSS_Hoffman.bedL2 0.0487 0.3134 0.5861 0.6907 0.2728 0.4503 0.4941 0.5635 0.6748 0.5709 0.5688 0.5570 0.5148 0.4194 0.4557 0.7340 0.7650 0.5945 0.5481 0.6465 0.6454 0.6781 0.6657 0.6881 0.6485 0.5884 0.8006 0.7903 0.7220 0.7806 0.7641 0.7426 0.4426 0.4557 0.6099 0.7143 TSS_Hoffman.extend.500.bedL2 0.0524 0.3417 0.6023 0.6961 0.3119 0.4849 0.5380 0.6033 0.7136 0.6128 0.6136 0.6008 0.5596 0.4278 0.4787 0.7729 0.8117 0.6354 0.5949 0.6889 0.6877 0.7212 0.7087 0.7338 0.6885 0.6281 0.8356 0.8313 0.7684 0.8205 0.8050 0.7862 0.4760 0.4887 0.6576 0.7722 UTR_3_UCSC.bedL2 0.0585 0.3566 0.8623 0.7603 0.2237 0.4239 0.5144 0.5669 0.5754 0.5542 0.5043 0.4954 0.5011 0.2472 0.2750 0.4924 0.5455 0.4892 0.4846 0.5387 0.5489 0.5573 0.5672 0.5573 0.5883 0.5741 0.6025 0.6286 0.6209 0.5858 0.6185 0.6405 0.4974 0.5104 0.4833 0.5928 UTR_3_UCSC.extend.500.bedL2 0.0526 0.3747 0.7590 0.7789 0.2042 0.4254 0.5302 0.5986 0.5774 0.5614 0.5001 0.4955 0.5007 0.2397 0.2677 0.4682 0.5301 0.4751 0.4787 0.5452 0.5582 0.5511 0.5639 0.5452 0.5881 0.5795 0.6031 0.6255 0.6141 0.5759 0.6109 0.6316 0.4944 0.5089 0.4958 0.5837 UTR_5_UCSC.bedL2 0.0364 0.2998 0.6060 0.6252 0.2023 0.3751 0.4223 0.4842 0.4897 0.4642 0.4223 0.4265 0.4174 0.2208 0.2424 0.4353 0.4683 0.4253 0.4132 0.4778 0.4860 0.4851 0.4912 0.4890 0.5086 0.4911 0.5343 0.5387 0.5193 0.5173 0.5403 0.5518 0.3849 0.3994 0.4383 0.4911 UTR_5_UCSC.extend.500.bedL2 0.0547 0.3680 0.6792 0.7854 0.2529 0.4632 0.5094 0.5892 0.6138 0.5781 0.5339 0.5272 0.5181 0.2627 0.2887 0.5334 0.5844 0.5259 0.5126 0.5951 0.6051 0.5959 0.6062 0.6107 0.6343 0.6112 0.6662 0.6688 0.6463 0.6273 0.6554 0.6736 0.4955 0.5109 0.5757 0.6340 WeakEnhancer_Hoffman.bedL2 0.0825 0.3530 0.4419 0.4839 0.3117 0.4821 0.5774 0.6213 0.7223 0.6425 0.6745 0.6667 0.6150 0.4132 0.4959 0.7329 0.7782 0.6893 0.6647 0.7010 0.7005 0.7173 0.7107 0.7747 0.7125 0.6583 0.7355 0.7280 0.7249 0.7459 0.7395 0.7437 0.5228 0.5285 0.5125 0.6080 WeakEnhancer_Hoffman.extend.500.bedL2 0.0996 0.4413 0.4794 0.5467 0.3924 0.5661 0.6453 0.7030 0.8201 0.7477 0.7679 0.7614 0.7167 0.4559 0.5535 0.8009 0.8520 0.7749 0.7601 0.7935 0.7964 0.8093 0.8080 0.8603 0.8146 0.7662 0.8001 0.8056 0.8132 0.8016 0.8050 0.8206 0.6122 0.6179 0.6177 0.7172 Promoter_UCSC.bedL2 Promoter_UCSC.extend.500.bedL2 Repressed_Hoffman.bedL2 Repressed_Hoffman.extend.500.bedL2 SuperEnhancer_Hnisz.bedL2 SuperEnhancer_Hnisz.extend.500.bedL2 TFBS_ENCODE.bedL2 TFBS_ENCODE.extend.500.bedL2 Transcribed_Hoffman.bedL2 Transcribed_Hoffman.extend.500.bedL2 TSS_Hoffman.bedL2 TSS_Hoffman.extend.500.bedL2 UTR_3_UCSC.bedL2 UTR_3_UCSC.extend.500.bedL2 UTR_5_UCSC.bedL2 UTR_5_UCSC.extend.500.bedL2 WeakEnhancer_Hoffman.bedL2 WeakEnhancer_Hoffman.extend.500.bedL2 MAF 0.0543 0.0584 0.1528 0.1597 0.0738 0.0746 0.1339 0.1570 0.0799 0.1420 0.0487 0.0524 0.0585 0.0526 0.0364 0.0547 0.0825 0.0996 baseL2 0.4343 0.4405 0.7969 0.8498 0.2928 0.2970 0.6043 0.7330 0.7267 0.9652 0.3134 0.3417 0.3566 0.3747 0.2998 0.3680 0.3530 0.4413 Coding_UCSC.bedL2 0.7386 0.7411 -0.0432 0.0110 0.3543 0.3575 0.5964 0.5600 0.5512 0.3581 0.5861 0.6023 0.8623 0.7590 0.6060 0.6792 0.4419 0.4794 Coding_UCSC.extend.500.bedL2 0.7786 0.7795 -0.0755 -0.0137 0.4472 0.4509 0.6980 0.6668 0.7001 0.4427 0.6907 0.6961 0.7603 0.7789 0.6252 0.7854 0.4839 0.5467 Conserved_LindbladToh.bedL2 0.2557 0.2591 0.3321 0.3841 0.2032 0.2067 0.4711 0.5278 0.5208 0.5725 0.2728 0.3119 0.2237 0.2042 0.2023 0.2529 0.3117 0.3924 Conserved_LindbladToh.extend.500.bedL2 0.4654 0.4661 0.4393 0.5077 0.4345 0.4388 0.7110 0.7821 0.7233 0.7698 0.4503 0.4849 0.4239 0.4254 0.3751 0.4632 0.4821 0.5661 CTCF_Hoffman.bedL2 0.5587 0.5639 0.1478 0.2149 0.5141 0.5181 0.7397 0.7460 0.5676 0.4796 0.4941 0.5380 0.5144 0.5302 0.4223 0.5094 0.5774 0.6453 CTCF_Hoffman.extend.500.bedL2 0.6445 0.6496 0.1960 0.2665 0.5653 0.5693 0.8080 0.8289 0.6464 0.5619 0.5635 0.6033 0.5669 0.5986 0.4842 0.5892 0.6213 0.7030 DGF_ENCODE.bedL2 0.6651 0.6656 0.1793 0.2588 0.7142 0.7179 0.9380 0.9521 0.7905 0.6588 0.6748 0.7136 0.5754 0.5774 0.4897 0.6138 0.7223 0.8201 DGF_ENCODE.extend.500.bedL2 0.6215 0.6255 0.3760 0.4581 0.6216 0.6262 0.8910 0.9593 0.8280 0.7961 0.5709 0.6128 0.5542 0.5614 0.4642 0.5781 0.6425 0.7477 DHS_peaks_Trynka.bedL2 0.5702 0.5695 0.2950 0.3719 0.6641 0.6680 0.8871 0.9292 0.7460 0.6986 0.5688 0.6136 0.5043 0.5001 0.4223 0.5339 0.6745 0.7679 DHS_Trynka.bedL2 0.5602 0.5609 0.3288 0.4058 0.6554 0.6593 0.8851 0.9343 0.7619 0.7291 0.5570 0.6008 0.4954 0.4955 0.4265 0.5272 0.6667 0.7614 DHS_Trynka.extend.500.bedL2 0.5558 0.5586 0.4503 0.5279 0.5829 0.5872 0.8560 0.9370 0.8117 0.8325 0.5148 0.5596 0.5011 0.5007 0.4174 0.5181 0.6150 0.7167 Enhancer_Andersson.bedL2 0.2966 0.2923 -0.0107 0.0220 0.5722 0.5725 0.4833 0.4556 0.2800 0.1909 0.4194 0.4278 0.2472 0.2397 0.2208 0.2627 0.4132 0.4559 Enhancer_Andersson.extend.500.bedL2 0.3369 0.3311 0.0059 0.0440 0.6638 0.6644 0.5805 0.5563 0.3445 0.2482 0.4557 0.4787 0.2750 0.2677 0.2424 0.2887 0.4959 0.5535 Enhancer_Hoffman.bedL2 0.5524 0.5449 -0.1619 -0.1043 0.7097 0.7106 0.8153 0.7416 0.6286 0.3629 0.7340 0.7729 0.4924 0.4682 0.4353 0.5334 0.7329 0.8009 Enhancer_Hoffman.extend.500.bedL2 0.6085 0.6017 -0.1531 -0.0844 0.7104 0.7118 0.8580 0.7954 0.6982 0.4191 0.7650 0.8117 0.5455 0.5301 0.4683 0.5844 0.7782 0.8520 FetalDHS_Trynka.bedL2 0.5575 0.5558 0.2339 0.3030 0.7010 0.7038 0.8696 0.8938 0.6980 0.6318 0.5945 0.6354 0.4892 0.4751 0.4253 0.5259 0.6893 0.7749 FetalDHS_Trynka.extend.500.bedL2 0.5498 0.5502 0.3301 0.4007 0.6720 0.6752 0.8694 0.9222 0.7470 0.7190 0.5481 0.5949 0.4846 0.4787 0.4132 0.5126 0.6647 0.7601 H3K27ac_Hnisz.bedL2 0.6181 0.6184 0.0086 0.0855 0.8294 0.8327 0.8795 0.8826 0.7122 0.5107 0.6465 0.6889 0.5387 0.5452 0.4778 0.5951 0.7010 0.7935 H3K27ac_Hnisz.extend.500.bedL2 0.6265 0.6275 0.0351 0.1138 0.8102 0.8137 0.8883 0.8977 0.7327 0.5391 0.6454 0.6877 0.5489 0.5582 0.4860 0.6051 0.7005 0.7964 H3K27ac_PGC2.bedL2 0.6242 0.6231 0.0282 0.1057 0.8380 0.8410 0.8959 0.8921 0.7287 0.5370 0.6781 0.7212 0.5573 0.5511 0.4851 0.5959 0.7173 0.8093 H3K27ac_PGC2.extend.500.bedL2 0.6320 0.6319 0.0512 0.1313 0.8149 0.8183 0.9011 0.9060 0.7494 0.5630 0.6657 0.7087 0.5672 0.5639 0.4912 0.6062 0.7107 0.8080 H3K4me1_peaks_Trynka.bedL2 0.6402 0.6399 0.0515 0.1314 0.7880 0.7907 0.9150 0.9178 0.7686 0.5759 0.6881 0.7338 0.5573 0.5452 0.4890 0.6107 0.7747 0.8603 H3K4me1_Trynka.bedL2 0.6614 0.6632 0.1529 0.2363 0.7327 0.7367 0.9172 0.9461 0.8066 0.6549 0.6485 0.6885 0.5883 0.5881 0.5086 0.6343 0.7125 0.8146 H3K4me1_Trynka.extend.500.bedL2 0.6348 0.6388 0.2924 0.3781 0.6400 0.6447 0.8889 0.9482 0.8342 0.7537 0.5884 0.6281 0.5741 0.5795 0.4911 0.6112 0.6583 0.7662 H3K4me3_peaks_Trynka.bedL2 0.7145 0.7057 0.0222 0.0975 0.7040 0.7063 0.8781 0.8374 0.7009 0.5190 0.8006 0.8356 0.6025 0.6031 0.5343 0.6662 0.7355 0.8001 H3K4me3_Trynka.bedL2 0.7355 0.7287 0.0447 0.1172 0.7128 0.7156 0.8990 0.8670 0.7364 0.5533 0.7903 0.8313 0.6286 0.6255 0.5387 0.6688 0.7280 0.8056 H3K4me3_Trynka.extend.500.bedL2 0.7140 0.7100 0.1430 0.2200 0.7130 0.7164 0.9114 0.9123 0.7823 0.6393 0.7220 0.7684 0.6209 0.6141 0.5193 0.6463 0.7249 0.8132 H3K9ac_peaks_Trynka.bedL2 0.6868 0.6829 -0.0952 -0.0303 0.7604 0.7620 0.8473 0.7914 0.6498 0.4148 0.7806 0.8205 0.5858 0.5759 0.5173 0.6273 0.7459 0.8016 H3K9ac_Trynka.bedL2 0.7116 0.7082 -0.0727 -0.0016 0.7806 0.7831 0.8764 0.8324 0.6775 0.4459 0.7641 0.8050 0.6185 0.6109 0.5403 0.6554 0.7395 0.8050 H3K9ac_Trynka.extend.500.bedL2 0.7240 0.7231 -0.0457 0.0303 0.7770 0.7801 0.8981 0.8723 0.7306 0.4948 0.7426 0.7862 0.6405 0.6316 0.5518 0.6736 0.7437 0.8206 Intron_UCSC.bedL2 0.4795 0.4891 0.1634 0.2599 0.5012 0.5054 0.6608 0.7131 0.7377 0.6336 0.4426 0.4760 0.4974 0.4944 0.3849 0.4955 0.5228 0.6122 Intron_UCSC.extend.500.bedL2 0.4936 0.5030 0.1597 0.2563 0.5050 0.5092 0.6700 0.7202 0.7435 0.6353 0.4557 0.4887 0.5104 0.5089 0.3994 0.5109 0.5285 0.6179 PromoterFlanking_Hoffman.bedL2 0.5956 0.5985 0.0072 0.0750 0.4277 0.4306 0.6579 0.6685 0.6818 0.4825 0.6099 0.6576 0.4833 0.4958 0.4383 0.5757 0.5125 0.6177 PromoterFlanking_Hoffman.extend.500.bedL2 0.6723 0.6712 0.0168 0.0943 0.4919 0.4958 0.7610 0.7568 0.7413 0.5368 0.7143 0.7722 0.5928 0.5837 0.4911 0.6340 0.6080 0.7172 Promoter_UCSC.bedL2 1.0000 0.9959 0.0327 0.0855 0.4651 0.4689 0.7056 0.6791 0.6090 0.4248 0.6998 0.7029 0.6482 0.7130 0.6549 0.7858 0.5110 0.5992 Promoter_UCSC.extend.500.bedL2 0.9959 1.0000 0.0386 0.0927 0.4630 0.4667 0.7019 0.6795 0.6136 0.4303 0.6878 0.6910 0.6513 0.7167 0.6536 0.7821 0.5067 0.5977 Repressed_Hoffman.bedL2 0.0327 0.0386 1.0000 0.9859 -0.0652 -0.0625 0.1101 0.2637 0.1903 0.6875 -0.1396 -0.1349 -0.0447 -0.0293 -0.0239 -0.0488 -0.0910 -0.0526 Repressed_Hoffman.extend.500.bedL2 0.0855 0.0927 0.9859 1.0000 -0.0088 -0.0058 0.1846 0.3444 0.2791 0.7567 -0.0893 -0.0763 0.0208 0.0328 0.0199 0.0066 -0.0209 0.0277 SuperEnhancer_Hnisz.bedL2 0.4651 0.4630 -0.0652 -0.0088 1.0000 0.9998 0.7035 0.6773 0.4659 0.3021 0.5597 0.5929 0.3904 0.3840 0.3746 0.4351 0.6106 0.6704 SuperEnhancer_Hnisz.extend.500.bedL2 0.4689 0.4667 -0.0625 -0.0058 0.9998 1.0000 0.7073 0.6816 0.4688 0.3055 0.5616 0.5948 0.3939 0.3885 0.3781 0.4388 0.6115 0.6721 TFBS_ENCODE.bedL2 0.7056 0.7019 0.1101 0.1846 0.7035 0.7073 1.0000 0.9637 0.7727 0.6138 0.7664 0.7991 0.6079 0.6234 0.5384 0.6655 0.7521 0.8401 TFBS_ENCODE.extend.500.bedL2 0.6791 0.6795 0.2637 0.3444 0.6773 0.6816 0.9637 1.0000 0.8185 0.7317 0.6676 0.7084 0.5848 0.6034 0.5097 0.6330 0.7101 0.8102 Transcribed_Hoffman.bedL2 0.6090 0.6136 0.1903 0.2791 0.4659 0.4688 0.7727 0.8185 1.0000 0.8232 0.6149 0.6465 0.5887 0.5966 0.4812 0.6078 0.6013 0.6928 Transcribed_Hoffman.extend.500.bedL2 0.4248 0.4303 0.6875 0.7567 0.3021 0.3055 0.6138 0.7317 0.8232 1.0000 0.3673 0.3972 0.3930 0.4007 0.3189 0.3915 0.3888 0.4725 TSS_Hoffman.bedL2 0.6998 0.6878 -0.1396 -0.0893 0.5597 0.5616 0.7664 0.6676 0.6149 0.3673 1.0000 0.9674 0.5586 0.5755 0.5549 0.6945 0.6186 0.6789 TSS_Hoffman.extend.500.bedL2 0.7029 0.6910 -0.1349 -0.0763 0.5929 0.5948 0.7991 0.7084 0.6465 0.3972 0.9674 1.0000 0.5898 0.5901 0.5434 0.6841 0.6730 0.7345 UTR_3_UCSC.bedL2 0.6482 0.6513 -0.0447 0.0208 0.3904 0.3939 0.6079 0.5848 0.5887 0.3930 0.5586 0.5898 1.0000 0.8617 0.5559 0.6135 0.4859 0.5302 UTR_3_UCSC.extend.500.bedL2 0.7130 0.7167 -0.0293 0.0328 0.3840 0.3885 0.6234 0.6034 0.5966 0.4007 0.5755 0.5901 0.8617 1.0000 0.6208 0.6873 0.4715 0.5225 UTR_5_UCSC.bedL2 0.6549 0.6536 -0.0239 0.0199 0.3746 0.3781 0.5384 0.5097 0.4812 0.3189 0.5549 0.5434 0.5559 0.6208 1.0000 0.8405 0.3939 0.4423 UTR_5_UCSC.extend.500.bedL2 0.7858 0.7821 -0.0488 0.0066 0.4351 0.4388 0.6655 0.6330 0.6078 0.3915 0.6945 0.6841 0.6135 0.6873 0.8405 1.0000 0.4907 0.5586 WeakEnhancer_Hoffman.bedL2 0.5110 0.5067 -0.0910 -0.0209 0.6106 0.6115 0.7521 0.7101 0.6013 0.3888 0.6186 0.6730 0.4859 0.4715 0.3939 0.4907 1.0000 0.9216 WeakEnhancer_Hoffman.extend.500.bedL2 0.5992 0.5977 -0.0526 0.0277 0.6704 0.6721 0.8401 0.8102 0.6928 0.4725 0.6789 0.7345 0.5302 0.5225 0.4423 0.5586 0.9216 1.0000 LD Score Matrix Condition Number 909.0712 Annotation Correlation Matrix base Coding_UCSC.bed Coding_UCSC.extend.500.bed Conserved_LindbladToh.bed Conserved_LindbladToh.extend.500.bed CTCF_Hoffman.bed CTCF_Hoffman.extend.500.bed DGF_ENCODE.bed DGF_ENCODE.extend.500.bed DHS_peaks_Trynka.bed DHS_Trynka.bed DHS_Trynka.extend.500.bed Enhancer_Andersson.bed Enhancer_Andersson.extend.500.bed Enhancer_Hoffman.bed Enhancer_Hoffman.extend.500.bed FetalDHS_Trynka.bed FetalDHS_Trynka.extend.500.bed H3K27ac_Hnisz.bed H3K27ac_Hnisz.extend.500.bed H3K27ac_PGC2.bed H3K27ac_PGC2.extend.500.bed H3K4me1_peaks_Trynka.bed H3K4me1_Trynka.bed H3K4me1_Trynka.extend.500.bed H3K4me3_peaks_Trynka.bed H3K4me3_Trynka.bed H3K4me3_Trynka.extend.500.bed H3K9ac_peaks_Trynka.bed H3K9ac_Trynka.bed H3K9ac_Trynka.extend.500.bed Intron_UCSC.bed Intron_UCSC.extend.500.bed PromoterFlanking_Hoffman.bed PromoterFlanking_Hoffman.extend.500.bed Promoter_UCSC.bed Promoter_UCSC.extend.500.bed Repressed_Hoffman.bed \ base NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN Coding_UCSC.bed NaN 1.0000 0.4633 0.2279 0.1400 0.0190 0.0276 0.0630 0.0590 0.0408 0.0470 0.0414 -0.0079 -0.0154 0.0390 0.0452 0.0476 0.0402 0.0630 0.0617 0.0631 0.0640 0.0472 0.0769 0.0651 0.0702 0.0894 0.0748 0.0636 0.0963 0.0926 -0.0704 0.0476 0.0076 0.0213 0.1358 0.1322 -0.0811 Coding_UCSC.extend.500.bed NaN 0.4633 1.0000 0.1171 0.3288 0.0218 0.0396 0.0817 0.1031 0.0639 0.0669 0.0744 -0.0147 -0.0209 0.0612 0.0786 0.0738 0.0687 0.1280 0.1273 0.1200 0.1266 0.0742 0.1489 0.1406 0.1021 0.1411 0.1278 0.1132 0.1723 0.1865 0.1715 0.2370 0.0194 0.0528 0.2482 0.2384 -0.1787 Conserved_LindbladToh.bed NaN 0.2279 0.1171 1.0000 0.2459 0.0075 0.0078 0.0872 0.0644 0.1358 0.1422 0.0937 0.0131 0.0089 0.0362 0.0343 0.1517 0.1096 0.0449 0.0434 0.0577 0.0516 0.0755 0.0951 0.0765 0.0576 0.0770 0.0630 0.0435 0.0741 0.0662 -0.0079 0.0352 0.0145 0.0200 0.0420 0.0399 -0.0313 Conserved_LindbladToh.extend.500.bed NaN 0.1400 0.3288 0.2459 1.0000 0.0526 0.0574 0.1188 0.1932 0.1762 0.2132 0.2672 0.0282 0.0483 0.1040 0.1162 0.2023 0.2830 0.1721 0.1738 0.1809 0.1784 0.1832 0.2640 0.2488 0.1107 0.1618 0.1588 0.1247 0.1976 0.2038 0.1385 0.1601 0.0301 0.0578 0.1005 0.0964 -0.1054 CTCF_Hoffman.bed NaN 0.0190 0.0218 0.0075 0.0526 1.0000 0.5676 0.1191 0.1164 0.1239 0.1321 0.1077 0.0128 0.0166 0.0387 0.0597 0.1300 0.1218 0.0518 0.0541 0.0506 0.0520 0.0795 0.0829 0.0722 0.0480 0.0659 0.0702 0.0671 0.0911 0.0998 -0.0014 0.0033 -0.0025 0.0224 0.0163 0.0181 -0.1366 CTCF_Hoffman.extend.500.bed NaN 0.0276 0.0396 0.0078 0.0574 0.5676 1.0000 0.0933 0.1660 0.0930 0.1028 0.1547 0.0149 0.0272 0.0585 0.0934 0.0974 0.1562 0.0880 0.0921 0.0871 0.0929 0.0912 0.1128 0.1177 0.0540 0.0814 0.1046 0.0808 0.1242 0.1517 0.0040 0.0097 0.0058 0.0357 0.0380 0.0429 -0.1304 DGF_ENCODE.bed NaN 0.0630 0.0817 0.0872 0.1188 0.1191 0.0933 1.0000 0.3702 0.5203 0.4995 0.2685 0.0910 0.0835 0.1941 0.1921 0.3560 0.2344 0.2141 0.2081 0.2380 0.2232 0.2914 0.2948 0.2253 0.1913 0.2592 0.2270 0.1746 0.2549 0.2436 0.0582 0.0720 0.0517 0.0928 0.1029 0.1041 -0.1807 DGF_ENCODE.extend.500.bed NaN 0.0590 0.1031 0.0644 0.1932 0.1164 0.1660 0.3702 1.0000 0.2718 0.3371 0.5714 0.0501 0.0954 0.1802 0.2433 0.2290 0.3884 0.3601 0.3653 0.3666 0.3667 0.3235 0.4832 0.4731 0.1593 0.2757 0.3357 0.1690 0.3012 0.3619 0.1090 0.1195 0.0667 0.1300 0.1051 0.1107 -0.2588 DHS_peaks_Trynka.bed NaN 0.0408 0.0639 0.1358 0.1762 0.1239 0.0930 0.5203 0.2718 1.0000 0.7726 0.3582 0.0997 0.0938 0.2132 0.1970 0.6547 0.3724 0.1995 0.1926 0.2355 0.2108 0.3084 0.3023 0.2255 0.2252 0.2752 0.2313 0.1989 0.2667 0.2363 0.0474 0.0590 0.0378 0.0867 0.0896 0.0836 -0.1492 DHS_Trynka.bed NaN 0.0470 0.0669 0.1422 0.2132 0.1321 0.1028 0.4995 0.3371 0.7726 1.0000 0.4541 0.0999 0.1098 0.2399 0.2253 0.6814 0.4386 0.2395 0.2314 0.2796 0.2509 0.3598 0.3685 0.2784 0.2436 0.3078 0.2669 0.2242 0.3047 0.2728 0.0574 0.0695 0.0413 0.0912 0.0918 0.0851 -0.1752 DHS_Trynka.extend.500.bed NaN 0.0414 0.0744 0.0937 0.2672 0.1077 0.1547 0.2685 0.5714 0.3582 0.4541 1.0000 0.0539 0.1017 0.1868 0.2472 0.3094 0.6381 0.3342 0.3401 0.3487 0.3385 0.3309 0.4990 0.4908 0.1524 0.2516 0.3139 0.1644 0.2861 0.3386 0.1063 0.1140 0.0448 0.1037 0.0844 0.0818 -0.2113 Enhancer_Andersson.bed NaN -0.0079 -0.0147 0.0131 0.0282 0.0128 0.0149 0.0910 0.0501 0.0997 0.0999 0.0539 1.0000 0.4723 0.1082 0.0961 0.1144 0.0698 0.0616 0.0589 0.0766 0.0669 0.0687 0.0579 0.0447 0.0694 0.0954 0.0744 0.0580 0.0877 0.0727 0.0157 0.0143 0.0126 0.0347 0.0211 0.0230 -0.0406 Enhancer_Andersson.extend.500.bed NaN -0.0154 -0.0209 0.0089 0.0483 0.0166 0.0272 0.0835 0.0954 0.0938 0.1098 0.1017 0.4723 1.0000 0.1733 0.1779 0.1116 0.1314 0.1210 0.1159 0.1479 0.1329 0.1189 0.1130 0.0873 0.1155 0.1604 0.1410 0.1141 0.1629 0.1405 0.0315 0.0291 0.0282 0.0565 0.0302 0.0378 -0.0748 Enhancer_Hoffman.bed NaN 0.0390 0.0612 0.0362 0.1040 0.0387 0.0585 0.1941 0.1802 0.2132 0.2399 0.1868 0.1082 0.1733 1.0000 0.6687 0.2267 0.2295 0.2169 0.2069 0.2947 0.2588 0.2564 0.2155 0.1557 0.2539 0.3121 0.2604 0.2377 0.3083 0.2635 0.0650 0.0730 0.0411 0.1361 0.1304 0.1264 -0.1829 Enhancer_Hoffman.extend.500.bed NaN 0.0452 0.0786 0.0343 0.1162 0.0597 0.0934 0.1921 0.2433 0.1970 0.2253 0.2472 0.0961 0.1779 0.6687 1.0000 0.2134 0.2821 0.3016 0.2972 0.4081 0.3733 0.2719 0.2906 0.2283 0.2397 0.3538 0.3551 0.2333 0.3646 0.3640 0.0859 0.0968 0.0985 0.2305 0.1844 0.1798 -0.2579 FetalDHS_Trynka.bed NaN 0.0476 0.0738 0.1517 0.2023 0.1300 0.0974 0.3560 0.2290 0.6547 0.6814 0.3094 0.1144 0.1116 0.2267 0.2134 1.0000 0.4850 0.2012 0.1927 0.2388 0.2126 0.3017 0.2857 0.2110 0.2667 0.3035 0.2509 0.2346 0.2930 0.2495 0.0433 0.0575 0.0381 0.0989 0.1138 0.1036 -0.1340 FetalDHS_Trynka.extend.500.bed NaN 0.0402 0.0687 0.1096 0.2830 0.1218 0.1562 0.2344 0.3884 0.3724 0.4386 0.6381 0.0698 0.1314 0.2295 0.2821 0.4850 1.0000 0.3199 0.3190 0.3509 0.3300 0.3456 0.4496 0.3901 0.2036 0.3042 0.3427 0.2084 0.3344 0.3596 0.0897 0.0988 0.0520 0.1210 0.1097 0.1016 -0.1832 H3K27ac_Hnisz.bed NaN 0.0630 0.1280 0.0449 0.1721 0.0518 0.0880 0.2141 0.3601 0.1995 0.2395 0.3342 0.0616 0.1210 0.2169 0.3016 0.2012 0.3199 1.0000 0.9401 0.5531 0.5848 0.3303 0.4925 0.4666 0.1704 0.2969 0.3650 0.2044 0.3671 0.4546 0.2403 0.2511 0.0698 0.1324 0.1300 0.1414 -0.3019 H3K27ac_Hnisz.extend.500.bed NaN 0.0617 0.1273 0.0434 0.1738 0.0541 0.0921 0.2081 0.3653 0.1926 0.2314 0.3401 0.0589 0.1159 0.2069 0.2972 0.1927 0.3190 0.9401 1.0000 0.5605 0.6041 0.3217 0.4976 0.4908 0.1630 0.2870 0.3645 0.1958 0.3554 0.4549 0.2362 0.2467 0.0694 0.1348 0.1279 0.1395 -0.3020 H3K27ac_PGC2.bed NaN 0.0631 0.1200 0.0577 0.1809 0.0506 0.0871 0.2380 0.3666 0.2355 0.2796 0.3487 0.0766 0.1479 0.2947 0.4081 0.2388 0.3509 0.5531 0.5605 1.0000 0.8560 0.3723 0.5087 0.4294 0.2356 0.4025 0.4725 0.2631 0.4682 0.5391 0.1908 0.2031 0.1009 0.1908 0.1743 0.1804 -0.2958 H3K27ac_PGC2.extend.500.bed NaN 0.0640 0.1266 0.0516 0.1784 0.0520 0.0929 0.2232 0.3667 0.2108 0.2509 0.3385 0.0669 0.1329 0.2588 0.3733 0.2126 0.3300 0.5848 0.6041 0.8560 1.0000 0.3534 0.5181 0.4647 0.2076 0.3645 0.4492 0.2357 0.4278 0.5232 0.2058 0.2174 0.0931 0.1800 0.1676 0.1780 -0.3039 H3K4me1_peaks_Trynka.bed NaN 0.0472 0.0742 0.0755 0.1832 0.0795 0.0912 0.2914 0.3235 0.3084 0.3598 0.3309 0.0687 0.1189 0.2564 0.2719 0.3017 0.3456 0.3303 0.3217 0.3723 0.3534 1.0000 0.5256 0.3691 0.2773 0.3822 0.3462 0.2985 0.4087 0.3785 0.1408 0.1486 0.1131 0.1615 0.1166 0.1195 -0.2345 H3K4me1_Trynka.bed NaN 0.0769 0.1489 0.0951 0.2640 0.0829 0.1128 0.2948 0.4832 0.3023 0.3685 0.4990 0.0579 0.1130 0.2155 0.2906 0.2857 0.4496 0.4925 0.4976 0.5087 0.5181 0.5256 1.0000 0.6964 0.1978 0.3491 0.4309 0.2214 0.4060 0.4953 0.2154 0.2281 0.0898 0.1586 0.1368 0.1453 -0.3154 H3K4me1_Trynka.extend.500.bed NaN 0.0651 0.1406 0.0765 0.2488 0.0722 0.1177 0.2253 0.4731 0.2255 0.2784 0.4908 0.0447 0.0873 0.1557 0.2283 0.2110 0.3901 0.4666 0.4908 0.4294 0.4647 0.3691 0.6964 1.0000 0.1394 0.2522 0.3472 0.1595 0.2977 0.4150 0.2315 0.2419 0.0649 0.1285 0.1149 0.1228 -0.2898 H3K4me3_peaks_Trynka.bed NaN 0.0702 0.1021 0.0576 0.1107 0.0480 0.0540 0.1913 0.1593 0.2252 0.2436 0.1524 0.0694 0.1155 0.2539 0.2397 0.2667 0.2036 0.1704 0.1630 0.2356 0.2076 0.2773 0.1978 0.1394 1.0000 0.5315 0.3610 0.3866 0.3610 0.2728 0.0543 0.0711 0.0984 0.1665 0.1794 0.1733 -0.1393 H3K4me3_Trynka.bed NaN 0.0894 0.1411 0.0770 0.1618 0.0659 0.0814 0.2592 0.2757 0.2752 0.3078 0.2516 0.0954 0.1604 0.3121 0.3538 0.3035 0.3042 0.2969 0.2870 0.4025 0.3645 0.3822 0.3491 0.2522 0.5315 1.0000 0.6705 0.3627 0.5577 0.4711 0.1050 0.1259 0.1702 0.2661 0.2484 0.2543 -0.2311 H3K4me3_Trynka.extend.500.bed NaN 0.0748 0.1278 0.0630 0.1588 0.0702 0.1046 0.2270 0.3357 0.2313 0.2669 0.3139 0.0744 0.1410 0.2604 0.3551 0.2509 0.3427 0.3650 0.3645 0.4725 0.4492 0.3462 0.4309 0.3472 0.3610 0.6705 1.0000 0.2777 0.4965 0.5557 0.1204 0.1359 0.1312 0.2442 0.2029 0.2124 -0.2575 H3K9ac_peaks_Trynka.bed NaN 0.0636 0.1132 0.0435 0.1247 0.0671 0.0808 0.1746 0.1690 0.1989 0.2242 0.1644 0.0580 0.1141 0.2377 0.2333 0.2346 0.2084 0.2044 0.1958 0.2631 0.2357 0.2985 0.2214 0.1595 0.3866 0.3627 0.2777 1.0000 0.5306 0.3714 0.0833 0.0973 0.0814 0.1429 0.1657 0.1635 -0.1557 H3K9ac_Trynka.bed NaN 0.0963 0.1723 0.0741 0.1976 0.0911 0.1242 0.2549 0.3012 0.2667 0.3047 0.2861 0.0877 0.1629 0.3083 0.3646 0.2930 0.3344 0.3671 0.3554 0.4682 0.4278 0.4087 0.4060 0.2977 0.3610 0.5577 0.4965 0.5306 1.0000 0.6951 0.1408 0.1610 0.1393 0.2298 0.2354 0.2413 -0.2641 H3K9ac_Trynka.extend.500.bed NaN 0.0926 0.1865 0.0662 0.2038 0.0998 0.1517 0.2436 0.3619 0.2363 0.2728 0.3386 0.0727 0.1405 0.2635 0.3640 0.2495 0.3596 0.4546 0.4549 0.5391 0.5232 0.3785 0.4953 0.4150 0.2728 0.4711 0.5557 0.3714 0.6951 1.0000 0.1814 0.1988 0.1194 0.2244 0.2123 0.2220 -0.3175 Intron_UCSC.bed NaN -0.0704 0.1715 -0.0079 0.1385 -0.0014 0.0040 0.0582 0.1090 0.0474 0.0574 0.1063 0.0157 0.0315 0.0650 0.0859 0.0433 0.0897 0.2403 0.2362 0.1908 0.2058 0.1408 0.2154 0.2315 0.0543 0.1050 0.1204 0.0833 0.1408 0.1814 1.0000 0.9796 0.0365 0.0377 0.0682 0.0784 -0.2562 Intron_UCSC.extend.500.bed NaN 0.0476 0.2370 0.0352 0.1601 0.0033 0.0097 0.0720 0.1195 0.0590 0.0695 0.1140 0.0143 0.0291 0.0730 0.0968 0.0575 0.0988 0.2511 0.2467 0.2031 0.2174 0.1486 0.2281 0.2419 0.0711 0.1259 0.1359 0.0973 0.1610 0.1988 0.9796 1.0000 0.0378 0.0459 0.1029 0.1111 -0.2690 PromoterFlanking_Hoffman.bed NaN 0.0076 0.0194 0.0145 0.0301 -0.0025 0.0058 0.0517 0.0667 0.0378 0.0413 0.0448 0.0126 0.0282 0.0411 0.0985 0.0381 0.0520 0.0698 0.0694 0.1009 0.0931 0.1131 0.0898 0.0649 0.0984 0.1702 0.1312 0.0814 0.1393 0.1194 0.0365 0.0378 1.0000 0.4982 0.1088 0.1215 -0.0803 PromoterFlanking_Hoffman.extend.500.bed NaN 0.0213 0.0528 0.0200 0.0578 0.0224 0.0357 0.0928 0.1300 0.0867 0.0912 0.1037 0.0347 0.0565 0.1361 0.2305 0.0989 0.1210 0.1324 0.1348 0.1908 0.1800 0.1615 0.1586 0.1285 0.1665 0.2661 0.2442 0.1429 0.2298 0.2244 0.0377 0.0459 0.4982 1.0000 0.2128 0.2191 -0.1397 Promoter_UCSC.bed NaN 0.1358 0.2482 0.0420 0.1005 0.0163 0.0380 0.1029 0.1051 0.0896 0.0918 0.0844 0.0211 0.0302 0.1304 0.1844 0.1138 0.1097 0.1300 0.1279 0.1743 0.1676 0.1166 0.1368 0.1149 0.1794 0.2484 0.2029 0.1657 0.2354 0.2123 0.0682 0.1029 0.1088 0.2128 1.0000 0.8994 -0.1203 Promoter_UCSC.extend.500.bed NaN 0.1322 0.2384 0.0399 0.0964 0.0181 0.0429 0.1041 0.1107 0.0836 0.0851 0.0818 0.0230 0.0378 0.1264 0.1798 0.1036 0.1016 0.1414 0.1395 0.1804 0.1780 0.1195 0.1453 0.1228 0.1733 0.2543 0.2124 0.1635 0.2413 0.2220 0.0784 0.1111 0.1215 0.2191 0.8994 1.0000 -0.1276 Repressed_Hoffman.bed NaN -0.0811 -0.1787 -0.0313 -0.1054 -0.1366 -0.1304 -0.1807 -0.2588 -0.1492 -0.1752 -0.2113 -0.0406 -0.0748 -0.1829 -0.2579 -0.1340 -0.1832 -0.3019 -0.3020 -0.2958 -0.3039 -0.2345 -0.3154 -0.2898 -0.1393 -0.2311 -0.2575 -0.1557 -0.2641 -0.3175 -0.2562 -0.2690 -0.0803 -0.1397 -0.1203 -0.1276 1.0000 Repressed_Hoffman.extend.500.bed NaN -0.1243 -0.2786 -0.0358 -0.1423 -0.0783 -0.1141 -0.2021 -0.2922 -0.1578 -0.1840 -0.2359 -0.0596 -0.1088 -0.2862 -0.3752 -0.1566 -0.2205 -0.4026 -0.4006 -0.4019 -0.4075 -0.2829 -0.3837 -0.3559 -0.1872 -0.3108 -0.3378 -0.2198 -0.3696 -0.4328 -0.3585 -0.3770 -0.1002 -0.1794 -0.1872 -0.1980 0.5921 SuperEnhancer_Hnisz.bed NaN 0.0417 0.0915 0.0197 0.1054 0.0317 0.0607 0.1599 0.2398 0.1268 0.1511 0.2050 0.0798 0.1464 0.1955 0.2581 0.1346 0.2092 0.5640 0.5303 0.4370 0.4383 0.2598 0.3459 0.3014 0.1507 0.2558 0.2842 0.1959 0.3251 0.3677 0.2321 0.2386 0.0417 0.0882 0.1065 0.1148 -0.2318 SuperEnhancer_Hnisz.extend.500.bed NaN 0.0420 0.0923 0.0193 0.1052 0.0332 0.0630 0.1595 0.2410 0.1255 0.1498 0.2050 0.0789 0.1454 0.1950 0.2603 0.1330 0.2089 0.5640 0.5360 0.4398 0.4427 0.2593 0.3480 0.3048 0.1498 0.2565 0.2867 0.1951 0.3256 0.3707 0.2316 0.2382 0.0439 0.0918 0.1094 0.1185 -0.2335 TFBS_ENCODE.bed NaN 0.0718 0.1091 0.0719 0.1408 0.2471 0.1893 0.3721 0.2929 0.3712 0.4245 0.2811 0.1042 0.1319 0.3234 0.3258 0.3453 0.2890 0.2387 0.2321 0.2868 0.2624 0.2930 0.2882 0.2204 0.2635 0.3432 0.2990 0.2354 0.3182 0.2931 0.0545 0.0714 0.0595 0.1392 0.1572 0.1529 -0.2330 TFBS_ENCODE.extend.500.bed NaN 0.0595 0.1007 0.0546 0.1668 0.1834 0.2854 0.2500 0.4370 0.2500 0.3055 0.4331 0.0670 0.1256 0.2637 0.3483 0.2361 0.3732 0.3316 0.3335 0.3728 0.3583 0.3037 0.3943 0.3541 0.1954 0.3216 0.3646 0.2003 0.3350 0.3701 0.0829 0.0948 0.0774 0.1620 0.1364 0.1377 -0.2739 Transcribed_Hoffman.bed NaN 0.0750 0.1817 0.0069 0.0428 -0.0317 -0.0092 0.0236 0.0609 -0.0141 -0.0109 0.0279 -0.0028 -0.0029 0.0060 0.0191 -0.0259 0.0015 0.1405 0.1406 0.1078 0.1244 0.0708 0.1259 0.1346 0.0029 0.0421 0.0642 0.0324 0.0702 0.1160 0.3294 0.3348 0.0006 -0.0085 0.0126 0.0231 -0.6175 Transcribed_Hoffman.extend.500.bed NaN 0.0151 0.0516 -0.0086 -0.0101 -0.0301 -0.0366 -0.0436 -0.0388 -0.0615 -0.0671 -0.0462 -0.0179 -0.0314 -0.0609 -0.0643 -0.0745 -0.0681 -0.0039 -0.0048 -0.0162 -0.0072 -0.0301 -0.0216 -0.0026 -0.0594 -0.0544 -0.0366 -0.0411 -0.0482 -0.0309 0.1940 0.1906 -0.0141 -0.0397 -0.0586 -0.0534 -0.2157 TSS_Hoffman.bed NaN 0.0938 0.1580 0.0431 0.0964 0.0253 0.0394 0.1773 0.1202 0.1937 0.1943 0.1229 0.0986 0.1280 0.1853 0.2557 0.2341 0.1726 0.1462 0.1383 0.2078 0.1790 0.1630 0.1387 0.1031 0.3125 0.3100 0.2174 0.2742 0.2907 0.2155 0.0382 0.0702 0.0787 0.2298 0.3308 0.3111 -0.1202 TSS_Hoffman.extend.500.bed NaN 0.0799 0.1436 0.0362 0.1021 0.0410 0.0663 0.1649 0.1591 0.1720 0.1790 0.1553 0.0892 0.1400 0.2745 0.3791 0.2094 0.2082 0.1937 0.1869 0.2722 0.2408 0.2030 0.1876 0.1408 0.2972 0.3772 0.2923 0.2689 0.3522 0.2908 0.0484 0.0747 0.1792 0.3613 0.3550 0.3403 -0.1648 UTR_3_UCSC.bed NaN 0.5777 0.2972 0.0615 0.0826 0.0129 0.0218 0.0380 0.0465 0.0223 0.0261 0.0332 -0.0069 -0.0137 0.0172 0.0261 0.0195 0.0270 0.0551 0.0563 0.0518 0.0529 0.0349 0.0605 0.0553 0.0301 0.0502 0.0488 0.0367 0.0644 0.0701 -0.0252 0.0147 0.0066 0.0102 0.0776 0.0801 -0.0650 UTR_3_UCSC.extend.500.bed NaN 0.4301 0.4502 0.0619 0.1363 0.0209 0.0331 0.0471 0.0616 0.0249 0.0283 0.0397 -0.0093 -0.0163 0.0251 0.0375 0.0247 0.0342 0.0755 0.0771 0.0715 0.0736 0.0426 0.0794 0.0753 0.0427 0.0730 0.0709 0.0527 0.0906 0.0993 0.0318 0.0731 0.0083 0.0207 0.1511 0.1515 -0.0961 UTR_5_UCSC.bed NaN 0.3322 0.1839 0.0769 0.0659 0.0020 0.0079 0.0525 0.0425 0.0483 0.0518 0.0361 -0.0051 -0.0092 0.0385 0.0468 0.0616 0.0416 0.0456 0.0442 0.0583 0.0550 0.0355 0.0542 0.0448 0.0813 0.0847 0.0650 0.0684 0.0836 0.0703 -0.0144 0.0477 0.0059 0.0344 0.2005 0.1869 -0.0516 UTR_5_UCSC.extend.500.bed NaN 0.1965 0.4526 0.0652 0.1602 0.0106 0.0209 0.0792 0.0757 0.0864 0.0884 0.0629 -0.0101 -0.0101 0.0790 0.0993 0.1097 0.0817 0.0874 0.0849 0.1107 0.1065 0.0677 0.0995 0.0873 0.1445 0.1580 0.1248 0.1285 0.1559 0.1376 0.0815 0.1350 0.0359 0.0934 0.4082 0.3803 -0.1039 WeakEnhancer_Hoffman.bed NaN 0.0113 0.0102 0.0181 0.0515 0.0399 0.0601 0.1565 0.1231 0.1587 0.1755 0.1230 0.0500 0.0646 0.1014 0.1595 0.1454 0.1330 0.1137 0.1099 0.1435 0.1312 0.2038 0.1465 0.1049 0.1314 0.1775 0.1547 0.1325 0.1731 0.1578 0.0349 0.0364 0.0207 0.0710 0.0343 0.0365 -0.1273 WeakEnhancer_Hoffman.extend.500.bed NaN 0.0143 0.0206 0.0250 0.0834 0.0830 0.1183 0.1617 0.2369 0.1666 0.1962 0.2343 0.0562 0.1036 0.2043 0.3034 0.1671 0.2352 0.2146 0.2126 0.2600 0.2507 0.2547 0.2677 0.2164 0.1448 0.2407 0.2763 0.1602 0.2518 0.2837 0.0656 0.0677 0.0576 0.1452 0.0637 0.0686 -0.2176 Repressed_Hoffman.extend.500.bed SuperEnhancer_Hnisz.bed SuperEnhancer_Hnisz.extend.500.bed TFBS_ENCODE.bed TFBS_ENCODE.extend.500.bed Transcribed_Hoffman.bed Transcribed_Hoffman.extend.500.bed TSS_Hoffman.bed TSS_Hoffman.extend.500.bed UTR_3_UCSC.bed UTR_3_UCSC.extend.500.bed UTR_5_UCSC.bed UTR_5_UCSC.extend.500.bed WeakEnhancer_Hoffman.bed WeakEnhancer_Hoffman.extend.500.bed base NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN Coding_UCSC.bed -0.1243 0.0417 0.0420 0.0718 0.0595 0.0750 0.0151 0.0938 0.0799 0.5777 0.4301 0.3322 0.1965 0.0113 0.0143 Coding_UCSC.extend.500.bed -0.2786 0.0915 0.0923 0.1091 0.1007 0.1817 0.0516 0.1580 0.1436 0.2972 0.4502 0.1839 0.4526 0.0102 0.0206 Conserved_LindbladToh.bed -0.0358 0.0197 0.0193 0.0719 0.0546 0.0069 -0.0086 0.0431 0.0362 0.0615 0.0619 0.0769 0.0652 0.0181 0.0250 Conserved_LindbladToh.extend.500.bed -0.1423 0.1054 0.1052 0.1408 0.1668 0.0428 -0.0101 0.0964 0.1021 0.0826 0.1363 0.0659 0.1602 0.0515 0.0834 CTCF_Hoffman.bed -0.0783 0.0317 0.0332 0.2471 0.1834 -0.0317 -0.0301 0.0253 0.0410 0.0129 0.0209 0.0020 0.0106 0.0399 0.0830 CTCF_Hoffman.extend.500.bed -0.1141 0.0607 0.0630 0.1893 0.2854 -0.0092 -0.0366 0.0394 0.0663 0.0218 0.0331 0.0079 0.0209 0.0601 0.1183 DGF_ENCODE.bed -0.2021 0.1599 0.1595 0.3721 0.2500 0.0236 -0.0436 0.1773 0.1649 0.0380 0.0471 0.0525 0.0792 0.1565 0.1617 DGF_ENCODE.extend.500.bed -0.2922 0.2398 0.2410 0.2929 0.4370 0.0609 -0.0388 0.1202 0.1591 0.0465 0.0616 0.0425 0.0757 0.1231 0.2369 DHS_peaks_Trynka.bed -0.1578 0.1268 0.1255 0.3712 0.2500 -0.0141 -0.0615 0.1937 0.1720 0.0223 0.0249 0.0483 0.0864 0.1587 0.1666 DHS_Trynka.bed -0.1840 0.1511 0.1498 0.4245 0.3055 -0.0109 -0.0671 0.1943 0.1790 0.0261 0.0283 0.0518 0.0884 0.1755 0.1962 DHS_Trynka.extend.500.bed -0.2359 0.2050 0.2050 0.2811 0.4331 0.0279 -0.0462 0.1229 0.1553 0.0332 0.0397 0.0361 0.0629 0.1230 0.2343 Enhancer_Andersson.bed -0.0596 0.0798 0.0789 0.1042 0.0670 -0.0028 -0.0179 0.0986 0.0892 -0.0069 -0.0093 -0.0051 -0.0101 0.0500 0.0562 Enhancer_Andersson.extend.500.bed -0.1088 0.1464 0.1454 0.1319 0.1256 -0.0029 -0.0314 0.1280 0.1400 -0.0137 -0.0163 -0.0092 -0.0101 0.0646 0.1036 Enhancer_Hoffman.bed -0.2862 0.1955 0.1950 0.3234 0.2637 0.0060 -0.0609 0.1853 0.2745 0.0172 0.0251 0.0385 0.0790 0.1014 0.2043 Enhancer_Hoffman.extend.500.bed -0.3752 0.2581 0.2603 0.3258 0.3483 0.0191 -0.0643 0.2557 0.3791 0.0261 0.0375 0.0468 0.0993 0.1595 0.3034 FetalDHS_Trynka.bed -0.1566 0.1346 0.1330 0.3453 0.2361 -0.0259 -0.0745 0.2341 0.2094 0.0195 0.0247 0.0616 0.1097 0.1454 0.1671 FetalDHS_Trynka.extend.500.bed -0.2205 0.2092 0.2089 0.2890 0.3732 0.0015 -0.0681 0.1726 0.2082 0.0270 0.0342 0.0416 0.0817 0.1330 0.2352 H3K27ac_Hnisz.bed -0.4026 0.5640 0.5640 0.2387 0.3316 0.1405 -0.0039 0.1462 0.1937 0.0551 0.0755 0.0456 0.0874 0.1137 0.2146 H3K27ac_Hnisz.extend.500.bed -0.4006 0.5303 0.5360 0.2321 0.3335 0.1406 -0.0048 0.1383 0.1869 0.0563 0.0771 0.0442 0.0849 0.1099 0.2126 H3K27ac_PGC2.bed -0.4019 0.4370 0.4398 0.2868 0.3728 0.1078 -0.0162 0.2078 0.2722 0.0518 0.0715 0.0583 0.1107 0.1435 0.2600 H3K27ac_PGC2.extend.500.bed -0.4075 0.4383 0.4427 0.2624 0.3583 0.1244 -0.0072 0.1790 0.2408 0.0529 0.0736 0.0550 0.1065 0.1312 0.2507 H3K4me1_peaks_Trynka.bed -0.2829 0.2598 0.2593 0.2930 0.3037 0.0708 -0.0301 0.1630 0.2030 0.0349 0.0426 0.0355 0.0677 0.2038 0.2547 H3K4me1_Trynka.bed -0.3837 0.3459 0.3480 0.2882 0.3943 0.1259 -0.0216 0.1387 0.1876 0.0605 0.0794 0.0542 0.0995 0.1465 0.2677 H3K4me1_Trynka.extend.500.bed -0.3559 0.3014 0.3048 0.2204 0.3541 0.1346 -0.0026 0.1031 0.1408 0.0553 0.0753 0.0448 0.0873 0.1049 0.2164 H3K4me3_peaks_Trynka.bed -0.1872 0.1507 0.1498 0.2635 0.1954 0.0029 -0.0594 0.3125 0.2972 0.0301 0.0427 0.0813 0.1445 0.1314 0.1448 H3K4me3_Trynka.bed -0.3108 0.2558 0.2565 0.3432 0.3216 0.0421 -0.0544 0.3100 0.3772 0.0502 0.0730 0.0847 0.1580 0.1775 0.2407 H3K4me3_Trynka.extend.500.bed -0.3378 0.2842 0.2867 0.2990 0.3646 0.0642 -0.0366 0.2174 0.2923 0.0488 0.0709 0.0650 0.1248 0.1547 0.2763 H3K9ac_peaks_Trynka.bed -0.2198 0.1959 0.1951 0.2354 0.2003 0.0324 -0.0411 0.2742 0.2689 0.0367 0.0527 0.0684 0.1285 0.1325 0.1602 H3K9ac_Trynka.bed -0.3696 0.3251 0.3256 0.3182 0.3350 0.0702 -0.0482 0.2907 0.3522 0.0644 0.0906 0.0836 0.1559 0.1731 0.2518 H3K9ac_Trynka.extend.500.bed -0.4328 0.3677 0.3707 0.2931 0.3701 0.1160 -0.0309 0.2155 0.2908 0.0701 0.0993 0.0703 0.1376 0.1578 0.2837 Intron_UCSC.bed -0.3585 0.2321 0.2316 0.0545 0.0829 0.3294 0.1940 0.0382 0.0484 -0.0252 0.0318 -0.0144 0.0815 0.0349 0.0656 Intron_UCSC.extend.500.bed -0.3770 0.2386 0.2382 0.0714 0.0948 0.3348 0.1906 0.0702 0.0747 0.0147 0.0731 0.0477 0.1350 0.0364 0.0677 PromoterFlanking_Hoffman.bed -0.1002 0.0417 0.0439 0.0595 0.0774 0.0006 -0.0141 0.0787 0.1792 0.0066 0.0083 0.0059 0.0359 0.0207 0.0576 PromoterFlanking_Hoffman.extend.500.bed -0.1794 0.0882 0.0918 0.1392 0.1620 -0.0085 -0.0397 0.2298 0.3613 0.0102 0.0207 0.0344 0.0934 0.0710 0.1452 Promoter_UCSC.bed -0.1872 0.1065 0.1094 0.1572 0.1364 0.0126 -0.0586 0.3308 0.3550 0.0776 0.1511 0.2005 0.4082 0.0343 0.0637 Promoter_UCSC.extend.500.bed -0.1980 0.1148 0.1185 0.1529 0.1377 0.0231 -0.0534 0.3111 0.3403 0.0801 0.1515 0.1869 0.3803 0.0365 0.0686 Repressed_Hoffman.bed 0.5921 -0.2318 -0.2335 -0.2330 -0.2739 -0.6175 -0.2157 -0.1202 -0.1648 -0.0650 -0.0961 -0.0516 -0.1039 -0.1273 -0.2176 Repressed_Hoffman.extend.500.bed 1.0000 -0.3341 -0.3361 -0.2776 -0.3255 -0.4519 -0.1354 -0.1999 -0.2592 -0.1008 -0.1478 -0.0780 -0.1626 -0.1477 -0.2566 SuperEnhancer_Hnisz.bed -0.3341 1.0000 0.9892 0.1895 0.2411 0.1348 0.0250 0.1506 0.1879 0.0354 0.0511 0.0348 0.0639 0.1031 0.1817 SuperEnhancer_Hnisz.extend.500.bed -0.3361 0.9892 1.0000 0.1895 0.2426 0.1352 0.0251 0.1493 0.1892 0.0362 0.0521 0.0344 0.0637 0.1028 0.1825 TFBS_ENCODE.bed -0.2776 0.1895 0.1895 1.0000 0.5449 0.0090 -0.0663 0.2889 0.2936 0.0382 0.0562 0.0677 0.1206 0.1834 0.2211 TFBS_ENCODE.extend.500.bed -0.3255 0.2411 0.2426 0.5449 1.0000 0.0409 -0.0524 0.1831 0.2421 0.0386 0.0582 0.0467 0.0919 0.1495 0.2788 Transcribed_Hoffman.bed -0.4519 0.1348 0.1352 0.0090 0.0409 1.0000 0.4529 -0.0396 -0.0276 0.0714 0.1016 0.0240 0.0514 0.0057 0.0171 Transcribed_Hoffman.extend.500.bed -0.1354 0.0250 0.0251 -0.0663 -0.0524 0.4529 1.0000 -0.0943 -0.0838 0.0249 0.0320 -0.0109 -0.0202 -0.0247 -0.0394 TSS_Hoffman.bed -0.1999 0.1506 0.1493 0.2889 0.1831 -0.0396 -0.0943 1.0000 0.7214 0.0254 0.0456 0.1371 0.2521 0.0586 0.0840 TSS_Hoffman.extend.500.bed -0.2592 0.1879 0.1892 0.2936 0.2421 -0.0276 -0.0838 0.7214 1.0000 0.0273 0.0504 0.1137 0.2238 0.0929 0.1466 UTR_3_UCSC.bed -0.1008 0.0354 0.0362 0.0382 0.0386 0.0714 0.0249 0.0254 0.0273 1.0000 0.6425 0.1101 0.0692 0.0120 0.0139 UTR_3_UCSC.extend.500.bed -0.1478 0.0511 0.0521 0.0562 0.0582 0.1016 0.0320 0.0456 0.0504 0.6425 1.0000 0.0976 0.1357 0.0151 0.0208 UTR_5_UCSC.bed -0.0780 0.0348 0.0344 0.0677 0.0467 0.0240 -0.0109 0.1371 0.1137 0.1101 0.0976 1.0000 0.4556 0.0111 0.0133 UTR_5_UCSC.extend.500.bed -0.1626 0.0639 0.0637 0.1206 0.0919 0.0514 -0.0202 0.2521 0.2238 0.0692 0.1357 0.4556 1.0000 0.0134 0.0237 WeakEnhancer_Hoffman.bed -0.1477 0.1031 0.1028 0.1834 0.1495 0.0057 -0.0247 0.0586 0.0929 0.0120 0.0151 0.0111 0.0134 1.0000 0.4722 WeakEnhancer_Hoffman.extend.500.bed -0.2566 0.1817 0.1825 0.2211 0.2788 0.0171 -0.0394 0.0840 0.1466 0.0139 0.0208 0.0133 0.0237 0.4722 1.0000 Annotation Matrix Column Sums base 438106.0 Coding_UCSC.bed 6599.0 Coding_UCSC.extend.500.bed 29140.0 Conserved_LindbladToh.bed 13028.0 Conserved_LindbladToh.extend.500.bed 147345.0 CTCF_Hoffman.bed 9783.0 CTCF_Hoffman.extend.500.bed 29001.0 DGF_ENCODE.bed 60640.0 DGF_ENCODE.extend.500.bed 236427.0 DHS_peaks_Trynka.bed 49777.0 DHS_Trynka.bed 74829.0 DHS_Trynka.extend.500.bed 218939.0 Enhancer_Andersson.bed 1800.0 Enhancer_Andersson.extend.500.bed 7957.0 Enhancer_Hoffman.bed 17133.0 Enhancer_Hoffman.extend.500.bed 36551.0 FetalDHS_Trynka.bed 38247.0 FetalDHS_Trynka.extend.500.bed 126663.0 H3K27ac_Hnisz.bed 178964.0 H3K27ac_Hnisz.extend.500.bed 192165.0 H3K27ac_PGC2.bed 122459.0 H3K27ac_PGC2.extend.500.bed 151668.0 H3K4me1_peaks_Trynka.bed 78930.0 H3K4me1_Trynka.bed 192287.0 H3K4me1_Trynka.extend.500.bed 270429.0 H3K4me3_peaks_Trynka.bed 18472.0 H3K4me3_Trynka.bed 57760.0 H3K4me3_Trynka.extend.500.bed 110631.0 H3K9ac_peaks_Trynka.bed 18900.0 H3K9ac_Trynka.bed 59750.0 H3K9ac_Trynka.extend.500.bed 107931.0 Intron_UCSC.bed 178258.0 Intron_UCSC.extend.500.bed 182636.0 PromoterFlanking_Hoffman.bed 3411.0 PromoterFlanking_Hoffman.extend.500.bed 13428.0 Promoter_UCSC.bed 20939.0 Promoter_UCSC.extend.500.bed 25594.0 Repressed_Hoffman.bed 197618.0 Repressed_Hoffman.extend.500.bed 307097.0 SuperEnhancer_Hnisz.bed 78911.0 SuperEnhancer_Hnisz.extend.500.bed 80322.0 TFBS_ENCODE.bed 56840.0 TFBS_ENCODE.extend.500.bed 146446.0 Transcribed_Hoffman.bed 140056.0 Transcribed_Hoffman.extend.500.bed 304968.0 TSS_Hoffman.bed 7568.0 TSS_Hoffman.extend.500.bed 14315.0 UTR_3_UCSC.bed 4930.0 UTR_3_UCSC.extend.500.bed 11755.0 UTR_5_UCSC.bed 2715.0 UTR_5_UCSC.extend.500.bed 12777.0 WeakEnhancer_Hoffman.bed 8479.0 WeakEnhancer_Hoffman.extend.500.bed 35620.0 Summary of Annotation Matrix Row Sums count 438106.0000 mean 11.2689 std 6.9757 min 1.0000 25% 6.0000 50% 9.0000 75% 15.0000 max 42.0000 Analysis finished at Tue Oct 17 17:31:34 2017 Total time elapsed: 50.0m:18.68s