********************************************************************* * 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.21.snp \ --ld-wind-cm 1.0 \ --out 1000G_Phase3_baseline_v1.1_rerun/baseline.21 \ --bfile 1000G_EUR_Phase3_plink/1000G.EUR.QC.21 \ --annot 1000G_Phase3_baseline_v1.1/baseline.21.annot.gz \ --l2 Beginning analysis at Tue Oct 17 16:41:15 2017 Read list of 138712 SNPs from 1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bim Read 53 annotations for 138712 SNPs from 1000G_Phase3_baseline_v1.1/baseline.21.annot.gz Read list of 489 individuals from 1000G_EUR_Phase3_plink/1000G.EUR.QC.21.fam Reading genotypes from 1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bed Estimating LD Score. Reading list of 19331 SNPs for which to print LD Scores from hapmap3_snps/hm.21.snp After merging with --print-snps, LD Scores for 16993 SNPs will be printed. Writing LD Scores for 16993 SNPs to 1000G_Phase3_baseline_v1.1_rerun/baseline.21.l2.ldscore.gz Summary of LD Scores in 1000G_Phase3_baseline_v1.1_rerun/baseline.21.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 0.2398 90.8622 1.3995 6.6591 2.3920 34.1678 2.0868 6.1158 13.1648 49.5808 10.5084 15.8943 46.2262 0.5998 2.5126 3.6301 7.9127 8.1694 26.8214 39.4649 42.3791 26.5710 33.0773 15.8096 41.1000 57.0121 3.8979 12.5585 24.5012 3.8958 13.1334 23.8277 35.1335 36.0179 0.6425 2.7385 5.1210 std 0.1429 68.8400 2.9376 13.0472 2.5328 31.1379 2.6375 6.9929 13.8715 45.0848 10.0638 14.6163 38.7063 1.1745 4.1571 5.0622 10.5916 8.0802 23.4751 45.9490 47.9705 30.1335 36.5481 17.5687 43.9537 55.0597 5.1037 15.5387 27.6990 6.0394 19.4116 32.8330 42.9251 44.0807 1.1845 4.3404 8.9249 min 0.0051 0.2805 -0.0738 -0.3463 -0.0861 -0.3892 -0.0907 -0.1613 -0.1180 0.1730 -0.1694 -0.1804 -0.1137 -0.1074 -0.2460 -0.1875 -0.2994 -0.1952 -0.2649 -0.5515 -0.5148 -0.3338 -0.2761 -0.1040 -0.2500 -0.1670 -0.1457 -0.3435 -0.1284 -0.1320 -0.5276 -0.5435 -1.7235 -1.7873 -0.0571 -0.1155 -0.2940 25% 0.1155 41.9645 0.0068 0.0786 0.6362 14.1064 0.3526 1.4529 4.1123 20.3400 4.0551 6.5509 21.0543 0.0212 0.1599 0.1006 0.4005 2.9560 11.4080 8.4082 10.2838 5.7692 7.8630 4.2655 13.1823 22.0540 0.7534 2.9801 7.4891 0.2878 1.3597 3.5585 2.2129 2.3323 0.0135 0.1216 0.1744 50% 0.2290 72.6797 0.1849 1.3199 1.6450 25.8640 1.1208 3.5923 8.3143 35.5084 7.3447 11.2605 35.1592 0.1442 0.9784 1.3331 3.2406 5.5845 19.8573 24.3850 26.9611 15.9616 20.4531 9.4806 26.5532 39.9911 1.9839 6.8151 14.5940 1.5352 5.4507 11.1417 18.9464 19.5234 0.1242 0.8515 1.4500 75% 0.3640 119.9862 1.4169 7.8527 3.1787 42.6608 2.7241 8.0952 17.0203 62.4313 13.4704 20.1119 58.6795 0.6258 2.9973 5.1206 11.3891 10.7151 34.8763 52.9051 56.3220 36.1292 44.6593 20.5231 51.5098 70.4765 4.9606 15.5183 30.1514 4.6792 15.9247 30.4106 54.4516 55.4503 0.7029 3.4190 5.9799 max 0.5000 476.9884 34.4921 131.1139 15.6453 234.4264 20.3885 46.2960 89.3082 290.9259 63.4111 98.0725 273.5884 9.6091 34.3426 32.0309 57.2579 53.8441 171.2025 296.0795 311.1975 211.1101 259.5591 119.9599 309.0572 379.6730 49.2789 110.0756 202.7895 55.9435 141.3161 230.4977 260.2749 281.5729 10.7887 36.3108 73.2266 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 6.4183 40.9870 63.7132 17.4620 17.7694 12.5709 31.9520 30.1272 66.5300 1.6450 3.1105 1.0080 2.7137 0.6180 3.1215 1.6940 6.8193 std 11.1485 39.1419 57.0790 27.1687 27.5017 13.4400 30.3519 37.3462 56.2452 3.2629 5.5691 2.1884 5.1031 1.3848 5.7822 2.6841 8.6951 min -0.3503 -0.4274 -0.6604 -0.6911 -0.7040 -0.1588 -0.1229 -0.5025 -0.7380 -0.1595 -0.2006 -0.1023 -0.2117 -0.0820 -0.2753 -0.1214 -0.1323 25% 0.2284 12.2240 21.9301 0.0568 0.0664 3.6836 11.9920 8.4540 26.7303 0.0116 0.0393 0.0103 0.0455 0.0084 0.1026 0.0717 0.7719 50% 1.8287 30.0735 48.3510 4.0937 4.2554 7.8116 21.9458 18.0168 50.4150 0.2361 0.5626 0.1460 0.5289 0.0817 0.7839 0.6068 3.3445 75% 7.4579 56.6897 89.2938 24.4468 24.8990 15.5448 40.7953 33.9388 90.3229 1.7350 3.7683 0.9941 3.0864 0.5194 3.4083 2.0804 9.5045 max 85.4901 270.2927 385.9059 225.6835 227.5070 82.9049 191.5015 308.6421 360.4834 37.0751 47.3724 22.1994 49.2187 20.8394 45.8777 22.9855 54.4285 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 0.2100 0.0772 0.0905 0.1149 0.1503 0.1612 0.1600 0.1599 0.1812 0.1758 0.1814 0.1879 0.0803 0.0964 0.1017 0.1209 0.1826 0.1926 0.1428 0.1473 0.1460 0.1489 0.1401 0.1470 0.1704 0.1132 0.1354 0.1470 0.1017 0.1091 0.1205 0.1379 0.1371 0.0660 0.1142 baseL2 0.2100 1.0000 0.4392 0.5107 0.6478 0.8431 0.6898 0.7056 0.7173 0.8374 0.7798 0.8097 0.8786 0.4042 0.4770 0.4428 0.5122 0.7479 0.8044 0.6863 0.7083 0.6664 0.6936 0.6818 0.7629 0.8294 0.5859 0.6223 0.6969 0.5604 0.6133 0.6507 0.5337 0.5399 0.5361 0.5515 Coding_UCSC.bedL2 0.0772 0.4392 1.0000 0.9086 0.3493 0.4107 0.5268 0.5687 0.6134 0.5794 0.5177 0.5004 0.5204 0.2423 0.3062 0.5129 0.5602 0.5186 0.4953 0.5684 0.5741 0.6074 0.6163 0.6076 0.6444 0.6026 0.6154 0.6313 0.6400 0.6833 0.6400 0.6605 0.5762 0.5962 0.5928 0.5952 Coding_UCSC.extend.500.bedL2 0.0905 0.5107 0.9086 1.0000 0.3764 0.5071 0.5825 0.6219 0.7124 0.6730 0.6146 0.5976 0.6131 0.3034 0.3681 0.5910 0.6461 0.6110 0.5902 0.6772 0.6813 0.7157 0.7246 0.7112 0.7489 0.7019 0.7001 0.7354 0.7370 0.7779 0.7427 0.7650 0.6885 0.7080 0.6981 0.7110 Conserved_LindbladToh.bedL2 0.1149 0.6478 0.3493 0.3764 1.0000 0.8365 0.4368 0.4372 0.5062 0.6303 0.5641 0.5831 0.6553 0.2969 0.3558 0.2884 0.3603 0.5007 0.5578 0.5688 0.5869 0.5282 0.5526 0.5166 0.6033 0.6580 0.3906 0.4365 0.4842 0.3690 0.4279 0.4624 0.4479 0.4522 0.4884 0.4997 Conserved_LindbladToh.extend.500.bedL2 0.1503 0.8431 0.4107 0.5071 0.8365 1.0000 0.6138 0.6009 0.6839 0.8184 0.7605 0.7833 0.8476 0.4200 0.4897 0.4651 0.5328 0.7103 0.7684 0.7351 0.7547 0.6931 0.7215 0.7032 0.7869 0.8414 0.5433 0.5978 0.6529 0.5220 0.5859 0.6261 0.5930 0.5971 0.6160 0.6227 CTCF_Hoffman.bedL2 0.1612 0.6898 0.5268 0.5825 0.4368 0.6138 1.0000 0.9443 0.7815 0.8009 0.7907 0.7897 0.7831 0.4089 0.5140 0.5665 0.6357 0.7920 0.7897 0.7264 0.7379 0.7027 0.7246 0.7514 0.7804 0.7904 0.7060 0.7120 0.7470 0.6884 0.7214 0.7515 0.5225 0.5320 0.5846 0.6468 CTCF_Hoffman.extend.500.bedL2 0.1600 0.7056 0.5687 0.6219 0.4372 0.6009 0.9443 1.0000 0.8260 0.8345 0.8171 0.8133 0.8094 0.4181 0.5244 0.6120 0.6734 0.8143 0.8142 0.7639 0.7745 0.7434 0.7648 0.7895 0.8124 0.8202 0.7528 0.7481 0.7920 0.7399 0.7672 0.8043 0.5367 0.5473 0.5728 0.6431 DGF_ENCODE.bedL2 0.1599 0.7173 0.6134 0.7124 0.5062 0.6839 0.7815 0.8260 1.0000 0.9576 0.9538 0.9448 0.9147 0.5993 0.7042 0.7775 0.8401 0.9112 0.9134 0.9201 0.9240 0.9364 0.9427 0.9531 0.9515 0.9297 0.9052 0.9116 0.9395 0.8913 0.9227 0.9394 0.6764 0.6864 0.6789 0.7480 DGF_ENCODE.extend.500.bedL2 0.1812 0.8374 0.5794 0.6730 0.6303 0.8184 0.8009 0.8345 0.9576 1.0000 0.9601 0.9679 0.9775 0.5691 0.6721 0.7164 0.7860 0.9165 0.9468 0.9302 0.9416 0.9172 0.9367 0.9338 0.9705 0.9805 0.8394 0.8646 0.9156 0.8226 0.8738 0.9060 0.6875 0.6961 0.6900 0.7434 DHS_peaks_Trynka.bedL2 0.1758 0.7798 0.5177 0.6146 0.5641 0.7605 0.7907 0.8171 0.9538 0.9601 1.0000 0.9887 0.9581 0.5960 0.6983 0.7307 0.7929 0.9630 0.9635 0.9170 0.9240 0.9048 0.9165 0.9389 0.9486 0.9491 0.8594 0.8643 0.9090 0.8366 0.8817 0.9024 0.6558 0.6630 0.6519 0.7132 DHS_Trynka.bedL2 0.1814 0.8097 0.5004 0.5976 0.5831 0.7833 0.7897 0.8133 0.9448 0.9679 0.9887 1.0000 0.9752 0.5970 0.6984 0.7122 0.7722 0.9589 0.9699 0.9098 0.9187 0.8942 0.9087 0.9249 0.9447 0.9539 0.8374 0.8487 0.8968 0.8110 0.8647 0.8866 0.6557 0.6623 0.6349 0.6905 DHS_Trynka.extend.500.bedL2 0.1879 0.8786 0.5204 0.6131 0.6553 0.8476 0.7831 0.8094 0.9147 0.9775 0.9581 0.9752 1.0000 0.5563 0.6569 0.6646 0.7342 0.9196 0.9617 0.8947 0.9087 0.8717 0.8931 0.8978 0.9440 0.9705 0.7906 0.8177 0.8775 0.7686 0.8280 0.8604 0.6765 0.6834 0.6543 0.6987 Enhancer_Andersson.bedL2 0.0803 0.4042 0.2423 0.3034 0.2969 0.4200 0.4089 0.4181 0.5993 0.5691 0.5960 0.5970 0.5563 1.0000 0.8961 0.5342 0.5634 0.5937 0.6035 0.5780 0.5745 0.6232 0.5952 0.5849 0.5694 0.5419 0.5965 0.5933 0.5675 0.5439 0.6209 0.5821 0.3536 0.3573 0.3601 0.4301 Enhancer_Andersson.extend.500.bedL2 0.0964 0.4770 0.3062 0.3681 0.3558 0.4897 0.5140 0.5244 0.7042 0.6721 0.6983 0.6984 0.6569 0.8961 1.0000 0.6243 0.6626 0.6946 0.6998 0.6832 0.6799 0.7209 0.6986 0.6835 0.6726 0.6464 0.6933 0.6863 0.6692 0.6395 0.7114 0.6757 0.4200 0.4252 0.4238 0.5059 Enhancer_Hoffman.bedL2 0.1017 0.4428 0.5129 0.5910 0.2884 0.4651 0.5665 0.6120 0.7775 0.7164 0.7307 0.7122 0.6646 0.5342 0.6243 1.0000 0.9651 0.7305 0.7047 0.7582 0.7496 0.8154 0.8024 0.8021 0.7576 0.7019 0.7732 0.7666 0.7579 0.7974 0.7712 0.7675 0.5715 0.5798 0.5980 0.6902 Enhancer_Hoffman.extend.500.bedL2 0.1209 0.5122 0.5602 0.6461 0.3603 0.5328 0.6357 0.6734 0.8401 0.7860 0.7929 0.7722 0.7342 0.5634 0.6626 0.9651 1.0000 0.7849 0.7650 0.8218 0.8161 0.8687 0.8601 0.8597 0.8244 0.7763 0.8113 0.8102 0.8076 0.8418 0.8279 0.8285 0.6128 0.6226 0.6640 0.7781 FetalDHS_Trynka.bedL2 0.1826 0.7479 0.5186 0.6110 0.5007 0.7103 0.7920 0.8143 0.9112 0.9165 0.9630 0.9589 0.9196 0.5937 0.6946 0.7305 0.7849 1.0000 0.9693 0.8848 0.8894 0.8719 0.8808 0.9212 0.9201 0.9153 0.8550 0.8503 0.8900 0.8473 0.8812 0.8948 0.6048 0.6134 0.6106 0.6859 FetalDHS_Trynka.extend.500.bedL2 0.1926 0.8044 0.4953 0.5902 0.5578 0.7684 0.7897 0.8142 0.9134 0.9468 0.9635 0.9699 0.9617 0.6035 0.6998 0.7047 0.7650 0.9693 1.0000 0.8942 0.9027 0.8767 0.8893 0.9186 0.9351 0.9439 0.8308 0.8418 0.8904 0.8085 0.8609 0.8817 0.6255 0.6327 0.6156 0.6831 H3K27ac_Hnisz.bedL2 0.1428 0.6863 0.5684 0.6772 0.5688 0.7351 0.7264 0.7639 0.9201 0.9302 0.9170 0.9098 0.8947 0.5780 0.6832 0.7582 0.8218 0.8848 0.8942 1.0000 0.9983 0.9535 0.9638 0.9537 0.9611 0.9402 0.8552 0.8683 0.9043 0.8619 0.9113 0.9300 0.6682 0.6784 0.6853 0.7420 H3K27ac_Hnisz.extend.500.bedL2 0.1473 0.7083 0.5741 0.6813 0.5869 0.7547 0.7379 0.7745 0.9240 0.9416 0.9240 0.9187 0.9087 0.5745 0.6799 0.7496 0.8161 0.8894 0.9027 0.9983 1.0000 0.9521 0.9651 0.9538 0.9682 0.9527 0.8523 0.8670 0.9066 0.8563 0.9075 0.9295 0.6738 0.6839 0.6933 0.7478 H3K27ac_PGC2.bedL2 0.1460 0.6664 0.6074 0.7157 0.5282 0.6931 0.7027 0.7434 0.9364 0.9172 0.9048 0.8942 0.8717 0.6232 0.7209 0.8154 0.8687 0.8719 0.8767 0.9535 0.9521 1.0000 0.9951 0.9543 0.9518 0.9158 0.8967 0.9025 0.9227 0.9001 0.9299 0.9336 0.6962 0.7071 0.6969 0.7591 H3K27ac_PGC2.extend.500.bedL2 0.1489 0.6936 0.6163 0.7246 0.5526 0.7215 0.7246 0.7648 0.9427 0.9367 0.9165 0.9087 0.8931 0.5952 0.6986 0.8024 0.8601 0.8808 0.8893 0.9638 0.9651 0.9951 1.0000 0.9592 0.9669 0.9381 0.8867 0.9002 0.9280 0.8930 0.9260 0.9384 0.7054 0.7163 0.7078 0.7670 H3K4me1_peaks_Trynka.bedL2 0.1401 0.6818 0.6076 0.7112 0.5166 0.7032 0.7514 0.7895 0.9531 0.9338 0.9389 0.9249 0.8978 0.5849 0.6835 0.8021 0.8597 0.9212 0.9186 0.9537 0.9538 0.9543 0.9592 1.0000 0.9719 0.9400 0.9156 0.9154 0.9382 0.9173 0.9376 0.9517 0.6920 0.7019 0.7039 0.7694 H3K4me1_Trynka.bedL2 0.1470 0.7629 0.6444 0.7489 0.6033 0.7869 0.7804 0.8124 0.9515 0.9705 0.9486 0.9447 0.9440 0.5694 0.6726 0.7576 0.8244 0.9201 0.9351 0.9611 0.9682 0.9518 0.9669 0.9719 1.0000 0.9858 0.8758 0.9013 0.9393 0.8822 0.9216 0.9483 0.7197 0.7306 0.7384 0.7880 H3K4me1_Trynka.extend.500.bedL2 0.1704 0.8294 0.6026 0.7019 0.6580 0.8414 0.7904 0.8202 0.9297 0.9805 0.9491 0.9539 0.9705 0.5419 0.6464 0.7019 0.7763 0.9153 0.9439 0.9402 0.9527 0.9158 0.9381 0.9400 0.9858 1.0000 0.8275 0.8561 0.9086 0.8238 0.8744 0.9108 0.7097 0.7192 0.7167 0.7655 H3K4me3_peaks_Trynka.bedL2 0.1132 0.5859 0.6154 0.7001 0.3906 0.5433 0.7060 0.7528 0.9052 0.8394 0.8594 0.8374 0.7906 0.5965 0.6933 0.7732 0.8113 0.8550 0.8308 0.8552 0.8523 0.8967 0.8867 0.9156 0.8758 0.8275 1.0000 0.9444 0.9321 0.9334 0.9309 0.9173 0.6104 0.6225 0.6501 0.7159 H3K4me3_Trynka.bedL2 0.1354 0.6223 0.6313 0.7354 0.4365 0.5978 0.7120 0.7481 0.9116 0.8646 0.8643 0.8487 0.8177 0.5933 0.6863 0.7666 0.8102 0.8503 0.8418 0.8683 0.8670 0.9025 0.9002 0.9154 0.9013 0.8561 0.9444 1.0000 0.9784 0.9162 0.9402 0.9309 0.6585 0.6704 0.6999 0.7504 H3K4me3_Trynka.extend.500.bedL2 0.1470 0.6969 0.6400 0.7370 0.4842 0.6529 0.7470 0.7920 0.9395 0.9156 0.9090 0.8968 0.8775 0.5675 0.6692 0.7579 0.8076 0.8900 0.8904 0.9043 0.9066 0.9227 0.9280 0.9382 0.9393 0.9086 0.9321 0.9784 1.0000 0.9147 0.9472 0.9546 0.6667 0.6786 0.7023 0.7467 H3K9ac_peaks_Trynka.bedL2 0.1017 0.5604 0.6833 0.7779 0.3690 0.5220 0.6884 0.7399 0.8913 0.8226 0.8366 0.8110 0.7686 0.5439 0.6395 0.7974 0.8418 0.8473 0.8085 0.8619 0.8563 0.9001 0.8930 0.9173 0.8822 0.8238 0.9334 0.9162 0.9147 1.0000 0.9627 0.9518 0.6346 0.6494 0.6583 0.7278 H3K9ac_Trynka.bedL2 0.1091 0.6133 0.6400 0.7427 0.4279 0.5859 0.7214 0.7672 0.9227 0.8738 0.8817 0.8647 0.8280 0.6209 0.7114 0.7712 0.8279 0.8812 0.8609 0.9113 0.9075 0.9299 0.9260 0.9376 0.9216 0.8744 0.9309 0.9402 0.9472 0.9627 1.0000 0.9864 0.6281 0.6422 0.6633 0.7304 H3K9ac_Trynka.extend.500.bedL2 0.1205 0.6507 0.6605 0.7650 0.4624 0.6261 0.7515 0.8043 0.9394 0.9060 0.9024 0.8866 0.8604 0.5821 0.6757 0.7675 0.8285 0.8948 0.8817 0.9300 0.9295 0.9336 0.9384 0.9517 0.9483 0.9108 0.9173 0.9309 0.9546 0.9518 0.9864 1.0000 0.6539 0.6678 0.6899 0.7563 Intron_UCSC.bedL2 0.1379 0.5337 0.5762 0.6885 0.4479 0.5930 0.5225 0.5367 0.6764 0.6875 0.6558 0.6557 0.6765 0.3536 0.4200 0.5715 0.6128 0.6048 0.6255 0.6682 0.6738 0.6962 0.7054 0.6920 0.7197 0.7097 0.6104 0.6585 0.6667 0.6346 0.6281 0.6539 1.0000 0.9994 0.6124 0.6405 Intron_UCSC.extend.500.bedL2 0.1371 0.5399 0.5962 0.7080 0.4522 0.5971 0.5320 0.5473 0.6864 0.6961 0.6630 0.6623 0.6834 0.3573 0.4252 0.5798 0.6226 0.6134 0.6327 0.6784 0.6839 0.7071 0.7163 0.7019 0.7306 0.7192 0.6225 0.6704 0.6786 0.6494 0.6422 0.6678 0.9994 1.0000 0.6246 0.6524 PromoterFlanking_Hoffman.bedL2 0.0660 0.5361 0.5928 0.6981 0.4884 0.6160 0.5846 0.5728 0.6789 0.6900 0.6519 0.6349 0.6543 0.3601 0.4238 0.5980 0.6640 0.6106 0.6156 0.6853 0.6933 0.6969 0.7078 0.7039 0.7384 0.7167 0.6501 0.6999 0.7023 0.6583 0.6633 0.6899 0.6124 0.6246 1.0000 0.9046 PromoterFlanking_Hoffman.extend.500.bedL2 0.1142 0.5515 0.5952 0.7110 0.4997 0.6227 0.6468 0.6431 0.7480 0.7434 0.7132 0.6905 0.6987 0.4301 0.5059 0.6902 0.7781 0.6859 0.6831 0.7420 0.7478 0.7591 0.7670 0.7694 0.7880 0.7655 0.7159 0.7504 0.7467 0.7278 0.7304 0.7563 0.6405 0.6524 0.9046 1.0000 Promoter_UCSC.bedL2 0.1069 0.5980 0.7163 0.7346 0.3861 0.5477 0.6393 0.6422 0.6313 0.6377 0.5931 0.5883 0.5976 0.3429 0.4019 0.5141 0.5750 0.6047 0.5757 0.5794 0.5853 0.6058 0.6132 0.6056 0.6495 0.6387 0.5914 0.6178 0.6228 0.5991 0.6055 0.6210 0.5469 0.5595 0.5972 0.6532 Promoter_UCSC.extend.500.bedL2 0.1048 0.5969 0.7201 0.7350 0.3803 0.5390 0.6445 0.6515 0.6349 0.6394 0.5935 0.5889 0.5984 0.3391 0.3979 0.5141 0.5749 0.6040 0.5764 0.5778 0.5839 0.6034 0.6117 0.6055 0.6495 0.6389 0.5939 0.6227 0.6267 0.6015 0.6081 0.6241 0.5462 0.5586 0.5951 0.6508 Repressed_Hoffman.bedL2 0.1640 0.7292 -0.0843 -0.0913 0.4163 0.5184 0.2467 0.2430 0.1324 0.3145 0.2636 0.3143 0.4085 0.0649 0.0728 -0.1399 -0.1075 0.2435 0.3207 0.1161 0.1407 0.0663 0.0940 0.0780 0.1749 0.2923 0.0007 0.0239 0.1127 -0.0676 0.0039 0.0350 0.0308 0.0270 0.0050 -0.0296 Repressed_Hoffman.extend.500.bedL2 0.1737 0.7820 -0.0545 -0.0498 0.4816 0.5926 0.3247 0.3168 0.2160 0.4016 0.3522 0.4037 0.4962 0.1390 0.1601 -0.0755 -0.0311 0.3261 0.4081 0.2074 0.2331 0.1512 0.1804 0.1635 0.2630 0.3819 0.0747 0.1003 0.1897 -0.0009 0.0823 0.1158 0.1033 0.0995 0.0725 0.0498 SuperEnhancer_Hnisz.bedL2 0.0985 0.3637 0.4012 0.4870 0.3269 0.4113 0.4541 0.4962 0.7179 0.6450 0.6631 0.6500 0.5962 0.5813 0.6708 0.6950 0.7058 0.6461 0.6284 0.7702 0.7483 0.8076 0.7785 0.7540 0.6977 0.6328 0.7447 0.7252 0.7063 0.7461 0.7693 0.7356 0.4839 0.4923 0.4568 0.5132 SuperEnhancer_Hnisz.extend.500.bedL2 0.0995 0.3662 0.4072 0.4926 0.3291 0.4127 0.4582 0.5010 0.7226 0.6491 0.6666 0.6534 0.5997 0.5798 0.6704 0.6972 0.7082 0.6497 0.6317 0.7731 0.7514 0.8105 0.7818 0.7578 0.7018 0.6367 0.7486 0.7290 0.7107 0.7505 0.7731 0.7400 0.4874 0.4960 0.4602 0.5166 TFBS_ENCODE.bedL2 0.1708 0.6755 0.6370 0.7294 0.4571 0.6350 0.7757 0.8083 0.9489 0.9113 0.9069 0.8974 0.8669 0.5966 0.7053 0.8193 0.8757 0.8925 0.8826 0.8917 0.8948 0.9106 0.9137 0.9245 0.9184 0.8897 0.8910 0.8929 0.9048 0.8860 0.9026 0.9096 0.6581 0.6688 0.6663 0.7616 TFBS_ENCODE.extend.500.bedL2 0.1773 0.7923 0.6189 0.7161 0.5635 0.7526 0.8054 0.8427 0.9602 0.9729 0.9472 0.9491 0.9475 0.6018 0.7019 0.7661 0.8353 0.9145 0.9327 0.9307 0.9380 0.9322 0.9426 0.9403 0.9629 0.9563 0.8647 0.8825 0.9197 0.8552 0.8985 0.9189 0.6951 0.7049 0.7072 0.7720 Transcribed_Hoffman.bedL2 0.1242 0.7263 0.7407 0.8494 0.5083 0.6938 0.6467 0.6639 0.7635 0.7867 0.7347 0.7317 0.7710 0.3748 0.4598 0.6590 0.7236 0.7214 0.7292 0.7540 0.7654 0.7784 0.7962 0.7885 0.8315 0.8205 0.7240 0.7735 0.7931 0.7869 0.7665 0.7935 0.7167 0.7306 0.7428 0.7635 Transcribed_Hoffman.extend.500.bedL2 0.1859 0.9544 0.4933 0.5754 0.6007 0.8028 0.6422 0.6483 0.6608 0.7732 0.7168 0.7436 0.8192 0.3594 0.4256 0.4335 0.5035 0.7023 0.7498 0.6309 0.6527 0.6249 0.6508 0.6448 0.7234 0.7822 0.5604 0.6085 0.6700 0.5620 0.5923 0.6264 0.5519 0.5599 0.5601 0.5679 TSS_Hoffman.bedL2 0.0922 0.4321 0.6296 0.7458 0.3270 0.4604 0.5299 0.5498 0.7035 0.6367 0.6286 0.5983 0.5785 0.4466 0.5282 0.7074 0.7605 0.6350 0.5967 0.6719 0.6695 0.7391 0.7226 0.7274 0.7016 0.6498 0.7780 0.7399 0.7048 0.7905 0.7364 0.7225 0.5717 0.5875 0.6402 0.7528 TSS_Hoffman.extend.500.bedL2 0.1109 0.4635 0.6379 0.7589 0.3453 0.4850 0.5722 0.6037 0.7520 0.6879 0.6850 0.6502 0.6293 0.4613 0.5405 0.7663 0.8195 0.6840 0.6518 0.7255 0.7226 0.7851 0.7700 0.7697 0.7496 0.6963 0.8008 0.7863 0.7636 0.8243 0.7818 0.7725 0.5944 0.6099 0.7029 0.8048 UTR_3_UCSC.bedL2 0.0865 0.3361 0.8092 0.7004 0.2003 0.2599 0.4926 0.5189 0.5537 0.4980 0.4820 0.4617 0.4548 0.2291 0.2875 0.5143 0.5339 0.4978 0.4639 0.4696 0.4758 0.5176 0.5207 0.5247 0.5465 0.5006 0.5632 0.5675 0.5738 0.6206 0.5809 0.5827 0.4179 0.4354 0.4843 0.4769 UTR_3_UCSC.extend.500.bedL2 0.0813 0.4583 0.8346 0.7759 0.3196 0.4024 0.5749 0.6030 0.6245 0.5987 0.5519 0.5412 0.5510 0.2997 0.3719 0.5559 0.5882 0.5606 0.5369 0.5568 0.5646 0.6003 0.6038 0.5938 0.6351 0.6017 0.6180 0.6292 0.6388 0.6509 0.6368 0.6441 0.5300 0.5469 0.5864 0.5802 UTR_5_UCSC.bedL2 0.1238 0.4324 0.5234 0.5993 0.2745 0.4210 0.5276 0.5287 0.5678 0.5699 0.5329 0.5327 0.5400 0.2494 0.2924 0.4678 0.5157 0.5421 0.5259 0.5528 0.5600 0.5394 0.5621 0.5773 0.5991 0.5875 0.5330 0.5618 0.5670 0.5518 0.5593 0.5890 0.5150 0.5258 0.5512 0.5854 UTR_5_UCSC.extend.500.bedL2 0.1238 0.5418 0.6821 0.7540 0.3855 0.5357 0.6660 0.6563 0.6724 0.6792 0.6363 0.6263 0.6398 0.3165 0.4047 0.5581 0.6359 0.6466 0.6186 0.6451 0.6561 0.6490 0.6694 0.6753 0.7174 0.7074 0.6407 0.6636 0.6677 0.6647 0.6703 0.6968 0.6201 0.6338 0.6683 0.7344 WeakEnhancer_Hoffman.bedL2 0.1209 0.3621 0.5404 0.5706 0.1298 0.2565 0.5726 0.6447 0.7502 0.6349 0.6653 0.6378 0.5750 0.4378 0.5246 0.7196 0.7455 0.6780 0.6341 0.6372 0.6311 0.6860 0.6791 0.7253 0.6595 0.5974 0.7432 0.7318 0.7305 0.7816 0.7494 0.7454 0.4546 0.4630 0.4451 0.5315 WeakEnhancer_Hoffman.extend.500.bedL2 0.1332 0.4367 0.5299 0.5875 0.2261 0.3694 0.6759 0.7287 0.8306 0.7300 0.7549 0.7291 0.6701 0.5001 0.5939 0.7868 0.8283 0.7535 0.7240 0.7209 0.7159 0.7712 0.7654 0.8087 0.7466 0.6933 0.8034 0.7886 0.7828 0.8154 0.7945 0.8014 0.5546 0.5613 0.5491 0.6607 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 0.1069 0.1048 0.1640 0.1737 0.0985 0.0995 0.1708 0.1773 0.1242 0.1859 0.0922 0.1109 0.0865 0.0813 0.1238 0.1238 0.1209 0.1332 baseL2 0.5980 0.5969 0.7292 0.7820 0.3637 0.3662 0.6755 0.7923 0.7263 0.9544 0.4321 0.4635 0.3361 0.4583 0.4324 0.5418 0.3621 0.4367 Coding_UCSC.bedL2 0.7163 0.7201 -0.0843 -0.0545 0.4012 0.4072 0.6370 0.6189 0.7407 0.4933 0.6296 0.6379 0.8092 0.8346 0.5234 0.6821 0.5404 0.5299 Coding_UCSC.extend.500.bedL2 0.7346 0.7350 -0.0913 -0.0498 0.4870 0.4926 0.7294 0.7161 0.8494 0.5754 0.7458 0.7589 0.7004 0.7759 0.5993 0.7540 0.5706 0.5875 Conserved_LindbladToh.bedL2 0.3861 0.3803 0.4163 0.4816 0.3269 0.3291 0.4571 0.5635 0.5083 0.6007 0.3270 0.3453 0.2003 0.3196 0.2745 0.3855 0.1298 0.2261 Conserved_LindbladToh.extend.500.bedL2 0.5477 0.5390 0.5184 0.5926 0.4113 0.4127 0.6350 0.7526 0.6938 0.8028 0.4604 0.4850 0.2599 0.4024 0.4210 0.5357 0.2565 0.3694 CTCF_Hoffman.bedL2 0.6393 0.6445 0.2467 0.3247 0.4541 0.4582 0.7757 0.8054 0.6467 0.6422 0.5299 0.5722 0.4926 0.5749 0.5276 0.6660 0.5726 0.6759 CTCF_Hoffman.extend.500.bedL2 0.6422 0.6515 0.2430 0.3168 0.4962 0.5010 0.8083 0.8427 0.6639 0.6483 0.5498 0.6037 0.5189 0.6030 0.5287 0.6563 0.6447 0.7287 DGF_ENCODE.bedL2 0.6313 0.6349 0.1324 0.2160 0.7179 0.7226 0.9489 0.9602 0.7635 0.6608 0.7035 0.7520 0.5537 0.6245 0.5678 0.6724 0.7502 0.8306 DGF_ENCODE.extend.500.bedL2 0.6377 0.6394 0.3145 0.4016 0.6450 0.6491 0.9113 0.9729 0.7867 0.7732 0.6367 0.6879 0.4980 0.5987 0.5699 0.6792 0.6349 0.7300 DHS_peaks_Trynka.bedL2 0.5931 0.5935 0.2636 0.3522 0.6631 0.6666 0.9069 0.9472 0.7347 0.7168 0.6286 0.6850 0.4820 0.5519 0.5329 0.6363 0.6653 0.7549 DHS_Trynka.bedL2 0.5883 0.5889 0.3143 0.4037 0.6500 0.6534 0.8974 0.9491 0.7317 0.7436 0.5983 0.6502 0.4617 0.5412 0.5327 0.6263 0.6378 0.7291 DHS_Trynka.extend.500.bedL2 0.5976 0.5984 0.4085 0.4962 0.5962 0.5997 0.8669 0.9475 0.7710 0.8192 0.5785 0.6293 0.4548 0.5510 0.5400 0.6398 0.5750 0.6701 Enhancer_Andersson.bedL2 0.3429 0.3391 0.0649 0.1390 0.5813 0.5798 0.5966 0.6018 0.3748 0.3594 0.4466 0.4613 0.2291 0.2997 0.2494 0.3165 0.4378 0.5001 Enhancer_Andersson.extend.500.bedL2 0.4019 0.3979 0.0728 0.1601 0.6708 0.6704 0.7053 0.7019 0.4598 0.4256 0.5282 0.5405 0.2875 0.3719 0.2924 0.4047 0.5246 0.5939 Enhancer_Hoffman.bedL2 0.5141 0.5141 -0.1399 -0.0755 0.6950 0.6972 0.8193 0.7661 0.6590 0.4335 0.7074 0.7663 0.5143 0.5559 0.4678 0.5581 0.7196 0.7868 Enhancer_Hoffman.extend.500.bedL2 0.5750 0.5749 -0.1075 -0.0311 0.7058 0.7082 0.8757 0.8353 0.7236 0.5035 0.7605 0.8195 0.5339 0.5882 0.5157 0.6359 0.7455 0.8283 FetalDHS_Trynka.bedL2 0.6047 0.6040 0.2435 0.3261 0.6461 0.6497 0.8925 0.9145 0.7214 0.7023 0.6350 0.6840 0.4978 0.5606 0.5421 0.6466 0.6780 0.7535 FetalDHS_Trynka.extend.500.bedL2 0.5757 0.5764 0.3207 0.4081 0.6284 0.6317 0.8826 0.9327 0.7292 0.7498 0.5967 0.6518 0.4639 0.5369 0.5259 0.6186 0.6341 0.7240 H3K27ac_Hnisz.bedL2 0.5794 0.5778 0.1161 0.2074 0.7702 0.7731 0.8917 0.9307 0.7540 0.6309 0.6719 0.7255 0.4696 0.5568 0.5528 0.6451 0.6372 0.7209 H3K27ac_Hnisz.extend.500.bedL2 0.5853 0.5839 0.1407 0.2331 0.7483 0.7514 0.8948 0.9380 0.7654 0.6527 0.6695 0.7226 0.4758 0.5646 0.5600 0.6561 0.6311 0.7159 H3K27ac_PGC2.bedL2 0.6058 0.6034 0.0663 0.1512 0.8076 0.8105 0.9106 0.9322 0.7784 0.6249 0.7391 0.7851 0.5176 0.6003 0.5394 0.6490 0.6860 0.7712 H3K27ac_PGC2.extend.500.bedL2 0.6132 0.6117 0.0940 0.1804 0.7785 0.7818 0.9137 0.9426 0.7962 0.6508 0.7226 0.7700 0.5207 0.6038 0.5621 0.6694 0.6791 0.7654 H3K4me1_peaks_Trynka.bedL2 0.6056 0.6055 0.0780 0.1635 0.7540 0.7578 0.9245 0.9403 0.7885 0.6448 0.7274 0.7697 0.5247 0.5938 0.5773 0.6753 0.7253 0.8087 H3K4me1_Trynka.bedL2 0.6495 0.6495 0.1749 0.2630 0.6977 0.7018 0.9184 0.9629 0.8315 0.7234 0.7016 0.7496 0.5465 0.6351 0.5991 0.7174 0.6595 0.7466 H3K4me1_Trynka.extend.500.bedL2 0.6387 0.6389 0.2923 0.3819 0.6328 0.6367 0.8897 0.9563 0.8205 0.7822 0.6498 0.6963 0.5006 0.6017 0.5875 0.7074 0.5974 0.6933 H3K4me3_peaks_Trynka.bedL2 0.5914 0.5939 0.0007 0.0747 0.7447 0.7486 0.8910 0.8647 0.7240 0.5604 0.7780 0.8008 0.5632 0.6180 0.5330 0.6407 0.7432 0.8034 H3K4me3_Trynka.bedL2 0.6178 0.6227 0.0239 0.1003 0.7252 0.7290 0.8929 0.8825 0.7735 0.6085 0.7399 0.7863 0.5675 0.6292 0.5618 0.6636 0.7318 0.7886 H3K4me3_Trynka.extend.500.bedL2 0.6228 0.6267 0.1127 0.1897 0.7063 0.7107 0.9048 0.9197 0.7931 0.6700 0.7048 0.7636 0.5738 0.6388 0.5670 0.6677 0.7305 0.7828 H3K9ac_peaks_Trynka.bedL2 0.5991 0.6015 -0.0676 -0.0009 0.7461 0.7505 0.8860 0.8552 0.7869 0.5620 0.7905 0.8243 0.6206 0.6509 0.5518 0.6647 0.7816 0.8154 H3K9ac_Trynka.bedL2 0.6055 0.6081 0.0039 0.0823 0.7693 0.7731 0.9026 0.8985 0.7665 0.5923 0.7364 0.7818 0.5809 0.6368 0.5593 0.6703 0.7494 0.7945 H3K9ac_Trynka.extend.500.bedL2 0.6210 0.6241 0.0350 0.1158 0.7356 0.7400 0.9096 0.9189 0.7935 0.6264 0.7225 0.7725 0.5827 0.6441 0.5890 0.6968 0.7454 0.8014 Intron_UCSC.bedL2 0.5469 0.5462 0.0308 0.1033 0.4839 0.4874 0.6581 0.6951 0.7167 0.5519 0.5717 0.5944 0.4179 0.5300 0.5150 0.6201 0.4546 0.5546 Intron_UCSC.extend.500.bedL2 0.5595 0.5586 0.0270 0.0995 0.4923 0.4960 0.6688 0.7049 0.7306 0.5599 0.5875 0.6099 0.4354 0.5469 0.5258 0.6338 0.4630 0.5613 PromoterFlanking_Hoffman.bedL2 0.5972 0.5951 0.0050 0.0725 0.4568 0.4602 0.6663 0.7072 0.7428 0.5601 0.6402 0.7029 0.4843 0.5864 0.5512 0.6683 0.4451 0.5491 PromoterFlanking_Hoffman.extend.500.bedL2 0.6532 0.6508 -0.0296 0.0498 0.5132 0.5166 0.7616 0.7720 0.7635 0.5679 0.7528 0.8048 0.4769 0.5802 0.5854 0.7344 0.5315 0.6607 Promoter_UCSC.bedL2 1.0000 0.9959 0.1810 0.2269 0.3781 0.3806 0.6608 0.6738 0.6587 0.6095 0.5907 0.6164 0.4924 0.6951 0.5190 0.7420 0.4655 0.5375 Promoter_UCSC.extend.500.bedL2 0.9959 1.0000 0.1776 0.2231 0.3764 0.3791 0.6645 0.6755 0.6564 0.6070 0.5848 0.6135 0.4984 0.6980 0.5156 0.7346 0.4739 0.5469 Repressed_Hoffman.bedL2 0.1810 0.1776 1.0000 0.9853 -0.1057 -0.1067 0.0804 0.2334 0.1228 0.6321 -0.1363 -0.1288 -0.1178 -0.0236 -0.0026 0.0225 -0.1571 -0.1246 Repressed_Hoffman.extend.500.bedL2 0.2269 0.2231 0.9853 1.0000 -0.0459 -0.0468 0.1595 0.3195 0.1901 0.6907 -0.0821 -0.0695 -0.0933 0.0143 0.0439 0.0820 -0.1050 -0.0524 SuperEnhancer_Hnisz.bedL2 0.3781 0.3764 -0.1057 -0.0459 1.0000 0.9998 0.7046 0.6871 0.4930 0.3096 0.5756 0.6069 0.3485 0.4055 0.3313 0.3760 0.5723 0.6313 SuperEnhancer_Hnisz.extend.500.bedL2 0.3806 0.3791 -0.1067 -0.0468 0.9998 1.0000 0.7088 0.6907 0.4975 0.3122 0.5785 0.6097 0.3550 0.4109 0.3350 0.3797 0.5779 0.6361 TFBS_ENCODE.bedL2 0.6608 0.6645 0.0804 0.1595 0.7046 0.7088 1.0000 0.9593 0.7648 0.6309 0.7598 0.8057 0.5827 0.6611 0.5641 0.7056 0.7683 0.8349 TFBS_ENCODE.extend.500.bedL2 0.6738 0.6755 0.2334 0.3195 0.6871 0.6907 0.9593 1.0000 0.7922 0.7367 0.6910 0.7489 0.5353 0.6414 0.5785 0.7055 0.6880 0.7783 Transcribed_Hoffman.bedL2 0.6587 0.6564 0.1228 0.1901 0.4930 0.4975 0.7648 0.7922 1.0000 0.8231 0.7203 0.7354 0.5864 0.6586 0.6031 0.7282 0.5462 0.5898 Transcribed_Hoffman.extend.500.bedL2 0.6095 0.6070 0.6321 0.6907 0.3096 0.3122 0.6309 0.7367 0.8231 1.0000 0.4719 0.4913 0.3685 0.4789 0.4595 0.5611 0.3443 0.4013 TSS_Hoffman.bedL2 0.5907 0.5848 -0.1363 -0.0821 0.5756 0.5785 0.7598 0.6910 0.7203 0.4719 1.0000 0.9565 0.4968 0.5747 0.5243 0.6685 0.5584 0.6290 TSS_Hoffman.extend.500.bedL2 0.6164 0.6135 -0.1288 -0.0695 0.6069 0.6097 0.8057 0.7489 0.7354 0.4913 0.9565 1.0000 0.5460 0.6196 0.5572 0.6881 0.6273 0.6877 UTR_3_UCSC.bedL2 0.4924 0.4984 -0.1178 -0.0933 0.3485 0.3550 0.5827 0.5353 0.5864 0.3685 0.4968 0.5460 1.0000 0.8826 0.4501 0.5653 0.5714 0.5299 UTR_3_UCSC.extend.500.bedL2 0.6951 0.6980 -0.0236 0.0143 0.4055 0.4109 0.6611 0.6414 0.6586 0.4789 0.5747 0.6196 0.8826 1.0000 0.5148 0.6926 0.5670 0.5649 UTR_5_UCSC.bedL2 0.5190 0.5156 -0.0026 0.0439 0.3313 0.3350 0.5641 0.5785 0.6031 0.4595 0.5243 0.5572 0.4501 0.5148 1.0000 0.8312 0.4146 0.4864 UTR_5_UCSC.extend.500.bedL2 0.7420 0.7346 0.0225 0.0820 0.3760 0.3797 0.7056 0.7055 0.7282 0.5611 0.6685 0.6881 0.5653 0.6926 0.8312 1.0000 0.4958 0.5778 WeakEnhancer_Hoffman.bedL2 0.4655 0.4739 -0.1571 -0.1050 0.5723 0.5779 0.7683 0.6880 0.5462 0.3443 0.5584 0.6273 0.5714 0.5670 0.4146 0.4958 1.0000 0.9176 WeakEnhancer_Hoffman.extend.500.bedL2 0.5375 0.5469 -0.1246 -0.0524 0.6313 0.6361 0.8349 0.7783 0.5898 0.4013 0.6290 0.6877 0.5299 0.5649 0.4864 0.5778 0.9176 1.0000 LD Score Matrix Condition Number 844.9655 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 0.4623 0.2433 0.1327 0.0096 0.0216 0.0641 0.0670 0.0416 0.0463 0.0414 -0.0098 -0.0179 0.0263 0.0291 0.0449 0.0328 0.0624 0.0624 0.0388 0.0448 0.0497 0.0920 0.0794 0.0598 0.0721 0.0671 0.0577 0.0763 0.0822 -0.0260 0.0817 0.0047 0.0097 0.1373 0.1297 -0.0908 Coding_UCSC.extend.500.bed NaN 0.4623 1.0000 0.1209 0.3084 0.0255 0.0438 0.1041 0.1359 0.0677 0.0729 0.0833 -0.0175 -0.0245 0.0456 0.0591 0.0747 0.0713 0.1404 0.1392 0.1013 0.1114 0.0813 0.1810 0.1658 0.0944 0.1373 0.1439 0.1079 0.1598 0.1973 0.2158 0.2749 0.0163 0.0370 0.2486 0.2370 -0.1938 Conserved_LindbladToh.bed NaN 0.2433 0.1209 1.0000 0.2236 0.0044 0.0016 0.0748 0.0548 0.1219 0.1241 0.0800 0.0137 0.0100 0.0293 0.0219 0.1298 0.0900 0.0374 0.0368 0.0473 0.0438 0.0598 0.0793 0.0609 0.0479 0.0583 0.0454 0.0375 0.0552 0.0428 -0.0088 0.0340 0.0161 0.0151 0.0404 0.0383 -0.0237 Conserved_LindbladToh.extend.500.bed NaN 0.1327 0.3084 0.2236 1.0000 0.0299 0.0252 0.0907 0.1622 0.1358 0.1661 0.2198 0.0222 0.0447 0.0650 0.0643 0.1503 0.2214 0.1284 0.1342 0.1429 0.1414 0.1316 0.2055 0.2073 0.0726 0.1098 0.1140 0.0800 0.1263 0.1352 0.1374 0.1551 0.0235 0.0374 0.0885 0.0818 -0.0758 CTCF_Hoffman.bed NaN 0.0096 0.0255 0.0044 0.0299 1.0000 0.5629 0.1218 0.1185 0.1276 0.1315 0.1125 0.0068 0.0187 0.0480 0.0695 0.1273 0.1184 0.0666 0.0656 0.0613 0.0647 0.0796 0.0847 0.0747 0.0597 0.0699 0.0845 0.0683 0.0930 0.1113 0.0062 0.0091 -0.0005 0.0176 0.0078 0.0121 -0.1402 CTCF_Hoffman.extend.500.bed NaN 0.0216 0.0438 0.0016 0.0252 0.5629 1.0000 0.1018 0.1680 0.1021 0.1079 0.1558 0.0106 0.0381 0.0721 0.1054 0.1049 0.1537 0.1021 0.1057 0.1003 0.1079 0.0981 0.1186 0.1146 0.0708 0.0974 0.1270 0.0885 0.1275 0.1635 0.0167 0.0206 0.0051 0.0411 0.0276 0.0293 -0.1366 DGF_ENCODE.bed NaN 0.0641 0.1041 0.0748 0.0907 0.1218 0.1018 1.0000 0.3855 0.5052 0.4871 0.2703 0.1085 0.1093 0.2083 0.2073 0.3504 0.2319 0.2404 0.2324 0.2600 0.2483 0.3023 0.3126 0.2409 0.2012 0.2774 0.2505 0.1845 0.2741 0.2695 0.0820 0.0956 0.0636 0.1036 0.1062 0.1089 -0.2098 DGF_ENCODE.extend.500.bed NaN 0.0670 0.1359 0.0548 0.1622 0.1185 0.1680 0.3855 1.0000 0.2683 0.3304 0.5492 0.0612 0.1198 0.1861 0.2565 0.2264 0.3803 0.4078 0.4062 0.3850 0.3903 0.3288 0.4971 0.4872 0.1651 0.2919 0.3531 0.1713 0.3178 0.3856 0.1592 0.1700 0.0671 0.1323 0.1182 0.1262 -0.2924 DHS_peaks_Trynka.bed NaN 0.0416 0.0677 0.1219 0.1358 0.1276 0.1021 0.5052 0.2683 1.0000 0.7730 0.3604 0.1212 0.1127 0.2184 0.2003 0.6571 0.3741 0.2045 0.1963 0.2421 0.2175 0.3145 0.3009 0.2286 0.2260 0.2739 0.2349 0.2083 0.2775 0.2503 0.0564 0.0681 0.0484 0.0871 0.0877 0.0836 -0.1596 DHS_Trynka.bed NaN 0.0463 0.0729 0.1241 0.1661 0.1315 0.1079 0.4871 0.3304 0.7730 1.0000 0.4570 0.1152 0.1261 0.2464 0.2318 0.6878 0.4398 0.2434 0.2351 0.2852 0.2557 0.3570 0.3636 0.2785 0.2443 0.3092 0.2690 0.2304 0.3149 0.2831 0.0665 0.0799 0.0558 0.0935 0.0945 0.0900 -0.1834 DHS_Trynka.extend.500.bed NaN 0.0414 0.0833 0.0800 0.2198 0.1125 0.1558 0.2703 0.5492 0.3604 0.4570 1.0000 0.0581 0.1212 0.1892 0.2535 0.3143 0.6486 0.3471 0.3509 0.3526 0.3456 0.3317 0.4862 0.4812 0.1564 0.2614 0.3205 0.1687 0.2993 0.3549 0.1298 0.1382 0.0487 0.1118 0.0879 0.0858 -0.2268 Enhancer_Andersson.bed NaN -0.0098 -0.0175 0.0137 0.0222 0.0068 0.0106 0.1085 0.0612 0.1212 0.1152 0.0581 1.0000 0.4859 0.1223 0.1039 0.1301 0.0801 0.0738 0.0693 0.0961 0.0859 0.0807 0.0742 0.0536 0.0791 0.1126 0.0912 0.0568 0.1027 0.0928 0.0081 0.0064 0.0169 0.0261 0.0167 0.0161 -0.0568 Enhancer_Andersson.extend.500.bed NaN -0.0179 -0.0245 0.0100 0.0447 0.0187 0.0381 0.1093 0.1198 0.1127 0.1261 0.1212 0.4859 1.0000 0.2008 0.2043 0.1279 0.1595 0.1464 0.1400 0.1921 0.1690 0.1423 0.1414 0.1054 0.1291 0.1897 0.1733 0.1289 0.1906 0.1739 0.0134 0.0122 0.0264 0.0638 0.0299 0.0321 -0.0990 Enhancer_Hoffman.bed NaN 0.0263 0.0456 0.0293 0.0650 0.0480 0.0721 0.2083 0.1861 0.2184 0.2464 0.1892 0.1223 0.2008 1.0000 0.6649 0.2264 0.2287 0.2189 0.2081 0.2993 0.2627 0.2673 0.2204 0.1628 0.2394 0.2914 0.2480 0.2380 0.3027 0.2560 0.0605 0.0682 0.0639 0.1628 0.1273 0.1296 -0.1920 Enhancer_Hoffman.extend.500.bed NaN 0.0291 0.0591 0.0219 0.0643 0.0695 0.1054 0.2073 0.2565 0.2003 0.2318 0.2535 0.1039 0.2043 0.6649 1.0000 0.2101 0.2804 0.3059 0.2986 0.4062 0.3734 0.2894 0.2971 0.2400 0.2267 0.3326 0.3365 0.2298 0.3635 0.3626 0.0782 0.0878 0.1124 0.2597 0.1757 0.1772 -0.2755 FetalDHS_Trynka.bed NaN 0.0449 0.0747 0.1298 0.1503 0.1273 0.1049 0.3504 0.2264 0.6571 0.6878 0.3143 0.1301 0.1279 0.2264 0.2101 1.0000 0.4846 0.1992 0.1888 0.2414 0.2121 0.3061 0.2857 0.2157 0.2584 0.3003 0.2477 0.2376 0.3010 0.2591 0.0434 0.0576 0.0467 0.0947 0.1015 0.0962 -0.1384 FetalDHS_Trynka.extend.500.bed NaN 0.0328 0.0713 0.0900 0.2214 0.1184 0.1537 0.2319 0.3803 0.3741 0.4398 0.6486 0.0801 0.1595 0.2287 0.2804 0.4846 1.0000 0.3173 0.3133 0.3509 0.3290 0.3495 0.4441 0.3959 0.2038 0.3135 0.3498 0.2118 0.3450 0.3725 0.0932 0.1026 0.0495 0.1209 0.1033 0.0990 -0.1917 H3K27ac_Hnisz.bed NaN 0.0624 0.1404 0.0374 0.1284 0.0666 0.1021 0.2404 0.4078 0.2045 0.2434 0.3471 0.0738 0.1464 0.2189 0.3059 0.1992 0.3173 1.0000 0.9421 0.5539 0.5913 0.3410 0.5107 0.4966 0.1729 0.3075 0.3859 0.1969 0.3778 0.4662 0.2409 0.2519 0.0608 0.1320 0.1200 0.1326 -0.3190 H3K27ac_Hnisz.extend.500.bed NaN 0.0624 0.1392 0.0368 0.1342 0.0656 0.1057 0.2324 0.4062 0.1963 0.2351 0.3509 0.0693 0.1400 0.2081 0.2986 0.1888 0.3133 0.9421 1.0000 0.5572 0.6065 0.3312 0.5111 0.5178 0.1643 0.2948 0.3825 0.1874 0.3637 0.4636 0.2399 0.2504 0.0608 0.1322 0.1170 0.1305 -0.3177 H3K27ac_PGC2.bed NaN 0.0388 0.1013 0.0473 0.1429 0.0613 0.1003 0.2600 0.3850 0.2421 0.2852 0.3526 0.0961 0.1921 0.2993 0.4062 0.2414 0.3509 0.5539 0.5572 1.0000 0.8524 0.3780 0.5088 0.4469 0.2380 0.4130 0.4747 0.2496 0.4633 0.5292 0.1903 0.2009 0.0943 0.1851 0.1721 0.1779 -0.3157 H3K27ac_PGC2.extend.500.bed NaN 0.0448 0.1114 0.0438 0.1414 0.0647 0.1079 0.2483 0.3903 0.2175 0.2557 0.3456 0.0859 0.1690 0.2627 0.3734 0.2121 0.3290 0.5913 0.6065 0.8524 1.0000 0.3599 0.5204 0.4860 0.2096 0.3743 0.4565 0.2225 0.4251 0.5176 0.2099 0.2206 0.0882 0.1786 0.1668 0.1761 -0.3265 H3K4me1_peaks_Trynka.bed NaN 0.0497 0.0813 0.0598 0.1316 0.0796 0.0981 0.3023 0.3288 0.3145 0.3570 0.3317 0.0807 0.1423 0.2673 0.2894 0.3061 0.3495 0.3410 0.3312 0.3780 0.3599 1.0000 0.5210 0.3727 0.2849 0.3931 0.3548 0.3022 0.4240 0.3931 0.1385 0.1469 0.1139 0.1746 0.1210 0.1250 -0.2511 H3K4me1_Trynka.bed NaN 0.0920 0.1810 0.0793 0.2055 0.0847 0.1186 0.3126 0.4971 0.3009 0.3636 0.4862 0.0742 0.1414 0.2204 0.2971 0.2857 0.4441 0.5107 0.5111 0.5088 0.5204 0.5210 1.0000 0.7095 0.2075 0.3674 0.4504 0.2263 0.4289 0.5279 0.2418 0.2549 0.0865 0.1641 0.1432 0.1507 -0.3462 H3K4me1_Trynka.extend.500.bed NaN 0.0794 0.1658 0.0609 0.2073 0.0747 0.1146 0.2409 0.4872 0.2286 0.2785 0.4812 0.0536 0.1054 0.1628 0.2400 0.2157 0.3959 0.4966 0.5178 0.4469 0.4860 0.3727 0.7095 1.0000 0.1494 0.2698 0.3755 0.1649 0.3181 0.4476 0.2499 0.2611 0.0645 0.1353 0.1245 0.1316 -0.3117 H3K4me3_peaks_Trynka.bed NaN 0.0598 0.0944 0.0479 0.0726 0.0597 0.0708 0.2012 0.1651 0.2260 0.2443 0.1564 0.0791 0.1291 0.2394 0.2267 0.2584 0.2038 0.1729 0.1643 0.2380 0.2096 0.2849 0.2075 0.1494 1.0000 0.5269 0.3555 0.3709 0.3500 0.2737 0.0598 0.0737 0.0898 0.1575 0.1536 0.1516 -0.1506 H3K4me3_Trynka.bed NaN 0.0721 0.1373 0.0583 0.1098 0.0699 0.0974 0.2774 0.2919 0.2739 0.3092 0.2614 0.1126 0.1897 0.2914 0.3326 0.3003 0.3135 0.3075 0.2948 0.4130 0.3743 0.3931 0.3674 0.2698 0.5269 1.0000 0.6679 0.3455 0.5416 0.4735 0.1235 0.1405 0.1581 0.2554 0.2227 0.2276 -0.2481 H3K4me3_Trynka.extend.500.bed NaN 0.0671 0.1439 0.0454 0.1140 0.0845 0.1270 0.2505 0.3531 0.2349 0.2690 0.3205 0.0912 0.1733 0.2480 0.3365 0.2477 0.3498 0.3859 0.3825 0.4747 0.4565 0.3548 0.4504 0.3755 0.3555 0.6679 1.0000 0.2681 0.4904 0.5619 0.1471 0.1602 0.1171 0.2356 0.1996 0.2061 -0.2829 H3K9ac_peaks_Trynka.bed NaN 0.0577 0.1079 0.0375 0.0800 0.0683 0.0885 0.1845 0.1713 0.2083 0.2304 0.1687 0.0568 0.1289 0.2380 0.2298 0.2376 0.2118 0.1969 0.1874 0.2496 0.2225 0.3022 0.2263 0.1649 0.3709 0.3455 0.2681 1.0000 0.5123 0.3609 0.0805 0.0929 0.0807 0.1357 0.1377 0.1397 -0.1579 H3K9ac_Trynka.bed NaN 0.0763 0.1598 0.0552 0.1263 0.0930 0.1275 0.2741 0.3178 0.2775 0.3149 0.2993 0.1027 0.1906 0.3027 0.3635 0.3010 0.3450 0.3778 0.3637 0.4633 0.4251 0.4240 0.4289 0.3181 0.3500 0.5416 0.4904 0.5123 1.0000 0.6974 0.1459 0.1632 0.1280 0.2289 0.2176 0.2249 -0.2767 H3K9ac_Trynka.extend.500.bed NaN 0.0822 0.1973 0.0428 0.1352 0.1113 0.1635 0.2695 0.3856 0.2503 0.2831 0.3549 0.0928 0.1739 0.2560 0.3626 0.2591 0.3725 0.4662 0.4636 0.5292 0.5176 0.3931 0.5279 0.4476 0.2737 0.4735 0.5619 0.3609 0.6974 1.0000 0.1955 0.2113 0.1144 0.2290 0.2204 0.2320 -0.3382 Intron_UCSC.bed NaN -0.0260 0.2158 -0.0088 0.1374 0.0062 0.0167 0.0820 0.1592 0.0564 0.0665 0.1298 0.0081 0.0134 0.0605 0.0782 0.0434 0.0932 0.2409 0.2399 0.1903 0.2099 0.1385 0.2418 0.2499 0.0598 0.1235 0.1471 0.0805 0.1459 0.1955 1.0000 0.9794 0.0386 0.0481 0.1180 0.1331 -0.2416 Intron_UCSC.extend.500.bed NaN 0.0817 0.2749 0.0340 0.1551 0.0091 0.0206 0.0956 0.1700 0.0681 0.0799 0.1382 0.0064 0.0122 0.0682 0.0878 0.0576 0.1026 0.2519 0.2504 0.2009 0.2206 0.1469 0.2549 0.2611 0.0737 0.1405 0.1602 0.0929 0.1632 0.2113 0.9794 1.0000 0.0403 0.0540 0.1486 0.1624 -0.2548 PromoterFlanking_Hoffman.bed NaN 0.0047 0.0163 0.0161 0.0235 -0.0005 0.0051 0.0636 0.0671 0.0484 0.0558 0.0487 0.0169 0.0264 0.0639 0.1124 0.0467 0.0495 0.0608 0.0608 0.0943 0.0882 0.1139 0.0865 0.0645 0.0898 0.1581 0.1171 0.0807 0.1280 0.1144 0.0386 0.0403 1.0000 0.4720 0.0959 0.1073 -0.0758 PromoterFlanking_Hoffman.extend.500.bed NaN 0.0097 0.0370 0.0151 0.0374 0.0176 0.0411 0.1036 0.1323 0.0871 0.0935 0.1118 0.0261 0.0638 0.1628 0.2597 0.0947 0.1209 0.1320 0.1322 0.1851 0.1786 0.1746 0.1641 0.1353 0.1575 0.2554 0.2356 0.1357 0.2289 0.2290 0.0481 0.0540 0.4720 1.0000 0.1933 0.2021 -0.1362 Promoter_UCSC.bed NaN 0.1373 0.2486 0.0404 0.0885 0.0078 0.0276 0.1062 0.1182 0.0877 0.0945 0.0879 0.0167 0.0299 0.1273 0.1757 0.1015 0.1033 0.1200 0.1170 0.1721 0.1668 0.1210 0.1432 0.1245 0.1536 0.2227 0.1996 0.1377 0.2176 0.2204 0.1180 0.1486 0.0959 0.1933 1.0000 0.8923 -0.1247 Promoter_UCSC.extend.500.bed NaN 0.1297 0.2370 0.0383 0.0818 0.0121 0.0293 0.1089 0.1262 0.0836 0.0900 0.0858 0.0161 0.0321 0.1296 0.1772 0.0962 0.0990 0.1326 0.1305 0.1779 0.1761 0.1250 0.1507 0.1316 0.1516 0.2276 0.2061 0.1397 0.2249 0.2320 0.1331 0.1624 0.1073 0.2021 0.8923 1.0000 -0.1327 Repressed_Hoffman.bed NaN -0.0908 -0.1938 -0.0237 -0.0758 -0.1402 -0.1366 -0.2098 -0.2924 -0.1596 -0.1834 -0.2268 -0.0568 -0.0990 -0.1920 -0.2755 -0.1384 -0.1917 -0.3190 -0.3177 -0.3157 -0.3265 -0.2511 -0.3462 -0.3117 -0.1506 -0.2481 -0.2829 -0.1579 -0.2767 -0.3382 -0.2416 -0.2548 -0.0758 -0.1362 -0.1247 -0.1327 1.0000 Repressed_Hoffman.extend.500.bed NaN -0.1413 -0.3086 -0.0298 -0.1062 -0.0760 -0.1229 -0.2490 -0.3495 -0.1772 -0.2033 -0.2564 -0.0750 -0.1351 -0.3066 -0.4022 -0.1645 -0.2302 -0.4251 -0.4218 -0.4296 -0.4377 -0.3106 -0.4363 -0.3929 -0.2041 -0.3385 -0.3775 -0.2263 -0.3920 -0.4670 -0.3472 -0.3673 -0.0941 -0.1839 -0.1932 -0.2077 0.5801 SuperEnhancer_Hnisz.bed NaN 0.0520 0.1165 0.0184 0.0724 0.0414 0.0695 0.2062 0.3009 0.1503 0.1758 0.2348 0.0873 0.1715 0.2089 0.2753 0.1469 0.2230 0.5906 0.5564 0.4423 0.4483 0.2809 0.3843 0.3448 0.1561 0.2852 0.3221 0.1826 0.3552 0.3986 0.2028 0.2122 0.0464 0.1013 0.0990 0.1101 -0.2598 SuperEnhancer_Hnisz.extend.500.bed NaN 0.0516 0.1177 0.0186 0.0733 0.0430 0.0726 0.2058 0.3029 0.1494 0.1745 0.2359 0.0864 0.1713 0.2072 0.2764 0.1466 0.2243 0.5904 0.5620 0.4442 0.4519 0.2802 0.3856 0.3483 0.1561 0.2845 0.3229 0.1820 0.3549 0.4018 0.2039 0.2134 0.0465 0.1044 0.1002 0.1122 -0.2612 TFBS_ENCODE.bed NaN 0.0576 0.1118 0.0578 0.0908 0.2377 0.1894 0.3824 0.3104 0.3616 0.4143 0.2866 0.1212 0.1651 0.3186 0.3310 0.3357 0.2824 0.2649 0.2570 0.3029 0.2820 0.3020 0.3015 0.2366 0.2640 0.3441 0.3025 0.2367 0.3242 0.3039 0.0769 0.0926 0.0763 0.1433 0.1506 0.1549 -0.2534 TFBS_ENCODE.extend.500.bed NaN 0.0504 0.1069 0.0362 0.1182 0.1812 0.2805 0.2687 0.4579 0.2457 0.2992 0.4299 0.0776 0.1561 0.2614 0.3538 0.2289 0.3569 0.3591 0.3586 0.3824 0.3723 0.3003 0.3954 0.3572 0.1954 0.3158 0.3639 0.1978 0.3359 0.3774 0.1154 0.1258 0.0771 0.1672 0.1418 0.1485 -0.2931 Transcribed_Hoffman.bed NaN 0.0878 0.1961 -0.0006 0.0390 -0.0183 0.0112 0.0360 0.0702 -0.0056 -0.0076 0.0262 -0.0095 -0.0213 -0.0234 -0.0087 -0.0244 -0.0053 0.1215 0.1248 0.0743 0.1022 0.0628 0.1367 0.1374 0.0056 0.0362 0.0672 0.0266 0.0570 0.1160 0.2725 0.2791 0.0005 -0.0114 0.0100 0.0193 -0.6134 Transcribed_Hoffman.extend.500.bed NaN 0.0239 0.0517 -0.0108 -0.0205 -0.0218 -0.0249 -0.0606 -0.0757 -0.0728 -0.0784 -0.0665 -0.0377 -0.0660 -0.0994 -0.1062 -0.0770 -0.0849 -0.0675 -0.0634 -0.0833 -0.0668 -0.0597 -0.0568 -0.0445 -0.0715 -0.0853 -0.0652 -0.0569 -0.0835 -0.0672 0.1195 0.1160 -0.0215 -0.0593 -0.0685 -0.0640 -0.1692 TSS_Hoffman.bed NaN 0.0706 0.1309 0.0277 0.0528 0.0303 0.0519 0.1758 0.1244 0.1873 0.1932 0.1202 0.0898 0.1129 0.1609 0.2402 0.2278 0.1654 0.1398 0.1320 0.2073 0.1788 0.1752 0.1375 0.1056 0.2898 0.2876 0.2048 0.2504 0.2762 0.2110 0.0549 0.0817 0.0807 0.2245 0.2880 0.2697 -0.1259 TSS_Hoffman.extend.500.bed NaN 0.0616 0.1218 0.0239 0.0555 0.0467 0.0834 0.1726 0.1676 0.1718 0.1833 0.1570 0.0863 0.1490 0.2772 0.3789 0.2072 0.2077 0.1925 0.1841 0.2761 0.2447 0.2154 0.1908 0.1485 0.2716 0.3504 0.2804 0.2510 0.3391 0.2887 0.0741 0.0961 0.1734 0.3501 0.3215 0.3103 -0.1755 UTR_3_UCSC.bed NaN 0.5712 0.2855 0.0615 0.0735 0.0116 0.0213 0.0426 0.0517 0.0271 0.0301 0.0338 -0.0085 -0.0136 0.0195 0.0295 0.0317 0.0314 0.0553 0.0549 0.0354 0.0393 0.0382 0.0708 0.0621 0.0320 0.0481 0.0477 0.0328 0.0538 0.0575 -0.0048 0.0389 -0.0002 0.0126 0.0671 0.0666 -0.0711 UTR_3_UCSC.extend.500.bed NaN 0.4252 0.4243 0.0675 0.1208 0.0189 0.0337 0.0588 0.0827 0.0365 0.0393 0.0576 -0.0082 -0.0148 0.0364 0.0491 0.0387 0.0493 0.0824 0.0811 0.0556 0.0561 0.0496 0.0933 0.0869 0.0461 0.0722 0.0754 0.0447 0.0771 0.0906 0.0580 0.0968 0.0075 0.0214 0.1617 0.1572 -0.1018 UTR_5_UCSC.bed NaN 0.2647 0.1475 0.0565 0.0405 0.0046 0.0131 0.0539 0.0440 0.0435 0.0498 0.0333 -0.0065 -0.0128 0.0360 0.0473 0.0495 0.0403 0.0546 0.0521 0.0484 0.0508 0.0427 0.0508 0.0421 0.0642 0.0822 0.0697 0.0651 0.0759 0.0703 0.0014 0.0597 0.0232 0.0403 0.1887 0.1813 -0.0502 UTR_5_UCSC.extend.500.bed NaN 0.1875 0.4233 0.0614 0.1256 0.0152 0.0314 0.0822 0.0893 0.0784 0.0865 0.0690 -0.0129 -0.0154 0.0759 0.0944 0.0987 0.0819 0.0888 0.0852 0.1034 0.1016 0.0776 0.1060 0.0946 0.1249 0.1530 0.1350 0.1178 0.1459 0.1471 0.1138 0.1646 0.0415 0.0842 0.4136 0.3862 -0.1059 WeakEnhancer_Hoffman.bed NaN 0.0168 0.0286 0.0106 0.0249 0.0327 0.0636 0.1670 0.1251 0.1631 0.1798 0.1278 0.0537 0.0803 0.1271 0.1824 0.1560 0.1326 0.1187 0.1165 0.1466 0.1417 0.2097 0.1505 0.1102 0.1252 0.1812 0.1590 0.1473 0.1915 0.1732 0.0276 0.0291 0.0274 0.0839 0.0387 0.0446 -0.1331 WeakEnhancer_Hoffman.extend.500.bed NaN 0.0220 0.0370 0.0102 0.0411 0.0854 0.1353 0.1846 0.2467 0.1742 0.2010 0.2395 0.0653 0.1230 0.2218 0.3172 0.1722 0.2378 0.2275 0.2258 0.2694 0.2630 0.2605 0.2723 0.2229 0.1520 0.2508 0.2849 0.1781 0.2737 0.3112 0.0554 0.0583 0.0625 0.1610 0.0753 0.0833 -0.2303 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 -0.1413 0.0520 0.0516 0.0576 0.0504 0.0878 0.0239 0.0706 0.0616 0.5712 0.4252 0.2647 0.1875 0.0168 0.0220 Coding_UCSC.extend.500.bed -0.3086 0.1165 0.1177 0.1118 0.1069 0.1961 0.0517 0.1309 0.1218 0.2855 0.4243 0.1475 0.4233 0.0286 0.0370 Conserved_LindbladToh.bed -0.0298 0.0184 0.0186 0.0578 0.0362 -0.0006 -0.0108 0.0277 0.0239 0.0615 0.0675 0.0565 0.0614 0.0106 0.0102 Conserved_LindbladToh.extend.500.bed -0.1062 0.0724 0.0733 0.0908 0.1182 0.0390 -0.0205 0.0528 0.0555 0.0735 0.1208 0.0405 0.1256 0.0249 0.0411 CTCF_Hoffman.bed -0.0760 0.0414 0.0430 0.2377 0.1812 -0.0183 -0.0218 0.0303 0.0467 0.0116 0.0189 0.0046 0.0152 0.0327 0.0854 CTCF_Hoffman.extend.500.bed -0.1229 0.0695 0.0726 0.1894 0.2805 0.0112 -0.0249 0.0519 0.0834 0.0213 0.0337 0.0131 0.0314 0.0636 0.1353 DGF_ENCODE.bed -0.2490 0.2062 0.2058 0.3824 0.2687 0.0360 -0.0606 0.1758 0.1726 0.0426 0.0588 0.0539 0.0822 0.1670 0.1846 DGF_ENCODE.extend.500.bed -0.3495 0.3009 0.3029 0.3104 0.4579 0.0702 -0.0757 0.1244 0.1676 0.0517 0.0827 0.0440 0.0893 0.1251 0.2467 DHS_peaks_Trynka.bed -0.1772 0.1503 0.1494 0.3616 0.2457 -0.0056 -0.0728 0.1873 0.1718 0.0271 0.0365 0.0435 0.0784 0.1631 0.1742 DHS_Trynka.bed -0.2033 0.1758 0.1745 0.4143 0.2992 -0.0076 -0.0784 0.1932 0.1833 0.0301 0.0393 0.0498 0.0865 0.1798 0.2010 DHS_Trynka.extend.500.bed -0.2564 0.2348 0.2359 0.2866 0.4299 0.0262 -0.0665 0.1202 0.1570 0.0338 0.0576 0.0333 0.0690 0.1278 0.2395 Enhancer_Andersson.bed -0.0750 0.0873 0.0864 0.1212 0.0776 -0.0095 -0.0377 0.0898 0.0863 -0.0085 -0.0082 -0.0065 -0.0129 0.0537 0.0653 Enhancer_Andersson.extend.500.bed -0.1351 0.1715 0.1713 0.1651 0.1561 -0.0213 -0.0660 0.1129 0.1490 -0.0136 -0.0148 -0.0128 -0.0154 0.0803 0.1230 Enhancer_Hoffman.bed -0.3066 0.2089 0.2072 0.3186 0.2614 -0.0234 -0.0994 0.1609 0.2772 0.0195 0.0364 0.0360 0.0759 0.1271 0.2218 Enhancer_Hoffman.extend.500.bed -0.4022 0.2753 0.2764 0.3310 0.3538 -0.0087 -0.1062 0.2402 0.3789 0.0295 0.0491 0.0473 0.0944 0.1824 0.3172 FetalDHS_Trynka.bed -0.1645 0.1469 0.1466 0.3357 0.2289 -0.0244 -0.0770 0.2278 0.2072 0.0317 0.0387 0.0495 0.0987 0.1560 0.1722 FetalDHS_Trynka.extend.500.bed -0.2302 0.2230 0.2243 0.2824 0.3569 -0.0053 -0.0849 0.1654 0.2077 0.0314 0.0493 0.0403 0.0819 0.1326 0.2378 H3K27ac_Hnisz.bed -0.4251 0.5906 0.5904 0.2649 0.3591 0.1215 -0.0675 0.1398 0.1925 0.0553 0.0824 0.0546 0.0888 0.1187 0.2275 H3K27ac_Hnisz.extend.500.bed -0.4218 0.5564 0.5620 0.2570 0.3586 0.1248 -0.0634 0.1320 0.1841 0.0549 0.0811 0.0521 0.0852 0.1165 0.2258 H3K27ac_PGC2.bed -0.4296 0.4423 0.4442 0.3029 0.3824 0.0743 -0.0833 0.2073 0.2761 0.0354 0.0556 0.0484 0.1034 0.1466 0.2694 H3K27ac_PGC2.extend.500.bed -0.4377 0.4483 0.4519 0.2820 0.3723 0.1022 -0.0668 0.1788 0.2447 0.0393 0.0561 0.0508 0.1016 0.1417 0.2630 H3K4me1_peaks_Trynka.bed -0.3106 0.2809 0.2802 0.3020 0.3003 0.0628 -0.0597 0.1752 0.2154 0.0382 0.0496 0.0427 0.0776 0.2097 0.2605 H3K4me1_Trynka.bed -0.4363 0.3843 0.3856 0.3015 0.3954 0.1367 -0.0568 0.1375 0.1908 0.0708 0.0933 0.0508 0.1060 0.1505 0.2723 H3K4me1_Trynka.extend.500.bed -0.3929 0.3448 0.3483 0.2366 0.3572 0.1374 -0.0445 0.1056 0.1485 0.0621 0.0869 0.0421 0.0946 0.1102 0.2229 H3K4me3_peaks_Trynka.bed -0.2041 0.1561 0.1561 0.2640 0.1954 0.0056 -0.0715 0.2898 0.2716 0.0320 0.0461 0.0642 0.1249 0.1252 0.1520 H3K4me3_Trynka.bed -0.3385 0.2852 0.2845 0.3441 0.3158 0.0362 -0.0853 0.2876 0.3504 0.0481 0.0722 0.0822 0.1530 0.1812 0.2508 H3K4me3_Trynka.extend.500.bed -0.3775 0.3221 0.3229 0.3025 0.3639 0.0672 -0.0652 0.2048 0.2804 0.0477 0.0754 0.0697 0.1350 0.1590 0.2849 H3K9ac_peaks_Trynka.bed -0.2263 0.1826 0.1820 0.2367 0.1978 0.0266 -0.0569 0.2504 0.2510 0.0328 0.0447 0.0651 0.1178 0.1473 0.1781 H3K9ac_Trynka.bed -0.3920 0.3552 0.3549 0.3242 0.3359 0.0570 -0.0835 0.2762 0.3391 0.0538 0.0771 0.0759 0.1459 0.1915 0.2737 H3K9ac_Trynka.extend.500.bed -0.4670 0.3986 0.4018 0.3039 0.3774 0.1160 -0.0672 0.2110 0.2887 0.0575 0.0906 0.0703 0.1471 0.1732 0.3112 Intron_UCSC.bed -0.3472 0.2028 0.2039 0.0769 0.1154 0.2725 0.1195 0.0549 0.0741 -0.0048 0.0580 0.0014 0.1138 0.0276 0.0554 Intron_UCSC.extend.500.bed -0.3673 0.2122 0.2134 0.0926 0.1258 0.2791 0.1160 0.0817 0.0961 0.0389 0.0968 0.0597 0.1646 0.0291 0.0583 PromoterFlanking_Hoffman.bed -0.0941 0.0464 0.0465 0.0763 0.0771 0.0005 -0.0215 0.0807 0.1734 -0.0002 0.0075 0.0232 0.0415 0.0274 0.0625 PromoterFlanking_Hoffman.extend.500.bed -0.1839 0.1013 0.1044 0.1433 0.1672 -0.0114 -0.0593 0.2245 0.3501 0.0126 0.0214 0.0403 0.0842 0.0839 0.1610 Promoter_UCSC.bed -0.1932 0.0990 0.1002 0.1506 0.1418 0.0100 -0.0685 0.2880 0.3215 0.0671 0.1617 0.1887 0.4136 0.0387 0.0753 Promoter_UCSC.extend.500.bed -0.2077 0.1101 0.1122 0.1549 0.1485 0.0193 -0.0640 0.2697 0.3103 0.0666 0.1572 0.1813 0.3862 0.0446 0.0833 Repressed_Hoffman.bed 0.5801 -0.2598 -0.2612 -0.2534 -0.2931 -0.6134 -0.1692 -0.1259 -0.1755 -0.0711 -0.1018 -0.0502 -0.1059 -0.1331 -0.2303 Repressed_Hoffman.extend.500.bed 1.0000 -0.3779 -0.3796 -0.3114 -0.3545 -0.4017 -0.0748 -0.2145 -0.2877 -0.1083 -0.1504 -0.0804 -0.1637 -0.1687 -0.2859 SuperEnhancer_Hnisz.bed -0.3779 1.0000 0.9900 0.2314 0.2884 0.1019 -0.0667 0.1375 0.1829 0.0506 0.0648 0.0381 0.0628 0.1076 0.2036 SuperEnhancer_Hnisz.extend.500.bed -0.3796 0.9900 1.0000 0.2318 0.2901 0.1026 -0.0672 0.1376 0.1841 0.0508 0.0661 0.0374 0.0633 0.1077 0.2039 TFBS_ENCODE.bed -0.3114 0.2314 0.2318 1.0000 0.5513 0.0177 -0.0796 0.2826 0.2960 0.0438 0.0627 0.0603 0.1162 0.1826 0.2364 TFBS_ENCODE.extend.500.bed -0.3545 0.2884 0.2901 0.5513 1.0000 0.0416 -0.0781 0.1835 0.2455 0.0438 0.0684 0.0503 0.0981 0.1445 0.2836 Transcribed_Hoffman.bed -0.4017 0.1019 0.1026 0.0177 0.0416 1.0000 0.4194 -0.0333 -0.0204 0.0763 0.0905 0.0248 0.0472 -0.0007 0.0011 Transcribed_Hoffman.extend.500.bed -0.0748 -0.0667 -0.0672 -0.0796 -0.0781 0.4194 1.0000 -0.0947 -0.0972 0.0280 0.0253 -0.0087 -0.0276 -0.0455 -0.0700 TSS_Hoffman.bed -0.2145 0.1375 0.1376 0.2826 0.1835 -0.0333 -0.0947 1.0000 0.7121 0.0252 0.0508 0.1327 0.2336 0.0734 0.0953 TSS_Hoffman.extend.500.bed -0.2877 0.1829 0.1841 0.2960 0.2455 -0.0204 -0.0972 0.7121 1.0000 0.0316 0.0543 0.1164 0.2250 0.1009 0.1579 UTR_3_UCSC.bed -0.1083 0.0506 0.0508 0.0438 0.0438 0.0763 0.0280 0.0252 0.0316 1.0000 0.6221 0.0597 0.0478 0.0131 0.0150 UTR_3_UCSC.extend.500.bed -0.1504 0.0648 0.0661 0.0627 0.0684 0.0905 0.0253 0.0508 0.0543 0.6221 1.0000 0.0494 0.1198 0.0203 0.0257 UTR_5_UCSC.bed -0.0804 0.0381 0.0374 0.0603 0.0503 0.0248 -0.0087 0.1327 0.1164 0.0597 0.0494 1.0000 0.4478 0.0157 0.0205 UTR_5_UCSC.extend.500.bed -0.1637 0.0628 0.0633 0.1162 0.0981 0.0472 -0.0276 0.2336 0.2250 0.0478 0.1198 0.4478 1.0000 0.0226 0.0469 WeakEnhancer_Hoffman.bed -0.1687 0.1076 0.1077 0.1826 0.1445 -0.0007 -0.0455 0.0734 0.1009 0.0131 0.0203 0.0157 0.0226 1.0000 0.4799 WeakEnhancer_Hoffman.extend.500.bed -0.2859 0.2036 0.2039 0.2364 0.2836 0.0011 -0.0700 0.0953 0.1579 0.0150 0.0257 0.0205 0.0469 0.4799 1.0000 Annotation Matrix Column Sums base 138712.0 Coding_UCSC.bed 2052.0 Coding_UCSC.extend.500.bed 9104.0 Conserved_LindbladToh.bed 3817.0 Conserved_LindbladToh.extend.500.bed 50122.0 CTCF_Hoffman.bed 3126.0 CTCF_Hoffman.extend.500.bed 9408.0 DGF_ENCODE.bed 20129.0 DGF_ENCODE.extend.500.bed 73962.0 DHS_peaks_Trynka.bed 15699.0 DHS_Trynka.bed 23619.0 DHS_Trynka.extend.500.bed 68751.0 Enhancer_Andersson.bed 881.0 Enhancer_Andersson.extend.500.bed 3656.0 Enhancer_Hoffman.bed 5709.0 Enhancer_Hoffman.extend.500.bed 12276.0 FetalDHS_Trynka.bed 12275.0 FetalDHS_Trynka.extend.500.bed 40569.0 H3K27ac_Hnisz.bed 59329.0 H3K27ac_Hnisz.extend.500.bed 63413.0 H3K27ac_PGC2.bed 40308.0 H3K27ac_PGC2.extend.500.bed 50011.0 H3K4me1_peaks_Trynka.bed 23948.0 H3K4me1_Trynka.bed 59727.0 H3K4me1_Trynka.extend.500.bed 83279.0 H3K4me3_peaks_Trynka.bed 6280.0 H3K4me3_Trynka.bed 19883.0 H3K4me3_Trynka.extend.500.bed 37841.0 H3K9ac_peaks_Trynka.bed 5730.0 H3K9ac_Trynka.bed 19224.0 H3K9ac_Trynka.extend.500.bed 34481.0 Intron_UCSC.bed 51472.0 Intron_UCSC.extend.500.bed 52824.0 PromoterFlanking_Hoffman.bed 921.0 PromoterFlanking_Hoffman.extend.500.bed 4041.0 Promoter_UCSC.bed 7358.0 Promoter_UCSC.extend.500.bed 9117.0 Repressed_Hoffman.bed 64079.0 Repressed_Hoffman.extend.500.bed 99651.0 SuperEnhancer_Hnisz.bed 28684.0 SuperEnhancer_Hnisz.extend.500.bed 29143.0 TFBS_ENCODE.bed 19243.0 TFBS_ENCODE.extend.500.bed 48044.0 Transcribed_Hoffman.bed 42718.0 Transcribed_Hoffman.extend.500.bed 99418.0 TSS_Hoffman.bed 2515.0 TSS_Hoffman.extend.500.bed 4874.0 UTR_3_UCSC.bed 1546.0 UTR_3_UCSC.extend.500.bed 3926.0 UTR_5_UCSC.bed 904.0 UTR_5_UCSC.extend.500.bed 4394.0 WeakEnhancer_Hoffman.bed 2803.0 WeakEnhancer_Hoffman.extend.500.bed 11401.0 Summary of Annotation Matrix Row Sums count 138712.0000 mean 11.4366 std 7.0600 min 1.0000 25% 6.0000 50% 10.0000 75% 16.0000 max 41.0000 Analysis finished at Tue Oct 17 16:54:31 2017 Total time elapsed: 13.0m:15.46s