Namespace(genes='/oak/stanford/groups/akundaje/soumyak/refs/gencode/hg38/hg38.gencode.protein_coding.tss.bed', list='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_summary/ldsc/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/ldsc/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.lymphocyte.H.overlap.peaks.bed.gz', schema='chrombpnet') Namespace(genes='/oak/stanford/groups/akundaje/soumyak/refs/gencode/hg38/hg38.gencode.protein_coding.tss.bed', list='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_summary/ldsc/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/ldsc/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.lymphocyte.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 1620045 chr1 11007 11008 G C chr1:11008:G:C 1620046 chr1 11011 11012 G C chr1:11012:G:C 1620047 chr1 13109 13110 A G chr1:13110:A:G 1620048 chr1 13115 13116 G T chr1:13116:G:T 1620049 chr1 13117 13118 G A chr1:13118:G:A Variants table shape: (4542891, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 10 \ 0 chr1 11007 11008 G C chr1:11008:G:C chr1 65419 65420 OR4F5 0 1 chr1 11007 11008 G C chr1:11008:G:C chr1 451677 451678 OR4F29 0 2 chr1 11007 11008 G C chr1:11008:G:C chr1 686653 686654 OR4F16 0 3 chr1 11011 11012 G C chr1:11012:G:C chr1 65419 65420 OR4F5 0 4 chr1 11011 11012 G C chr1:11012:G:C chr1 451677 451678 OR4F29 0 11 12 13 14 0 + ENSG00000186092.7 protein_coding 54412 1 - ENSG00000284733.2 protein_coding 440670 2 - ENSG00000284662.2 protein_coding 675646 3 + ENSG00000186092.7 protein_coding 54408 4 - ENSG00000284733.2 protein_coding 440666 Closest genes table shape: (13628673, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 778638 778639 G A chr1:778639:G:A 1 chr1 904972 904973 C G chr1:904973:C:G 2 chr1 959338 959339 T C chr1:959339:T:C 3 chr1 960508 960509 T A chr1:960509:T:A 4 chr1 966907 966908 A G chr1:966908:A:G Peak overlap table shape: (25723, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 14744 C A chr10:14744:C:A -0.021704 0.207057 1 chr10 15391 G A chr10:15391:G:A -0.030460 0.132411 2 chr10 15394 A G chr10:15394:A:G 0.000296 0.814831 3 chr10 15479 A G chr10:15479:A:G -0.008422 0.514785 4 chr10 17274 C G chr10:17274:C:G -0.000398 0.872798 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.021704 0.239310 0.011961 ... 1 0.030460 0.155120 0.014834 ... 2 0.002885 0.824758 0.005286 ... 3 0.008422 0.569116 0.012939 ... 4 0.002040 0.881718 0.005002 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.325282 0.003853 1 0.360750 0.003465 2 0.885639 0.000348 3 0.705629 0.000950 4 0.798062 0.000789 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.368162 TUBB8 59419 1 0.406708 TUBB8 58772 2 0.898483 TUBB8 58769 3 0.767540 TUBB8 58684 4 0.802839 TUBB8 56889 closest_gene_2 gene_distance_2 closest_gene_3 gene_distance_3 \ 0 ZMYND11 115345 DIP2C 674924 1 ZMYND11 114698 DIP2C 674277 2 ZMYND11 114695 DIP2C 674274 3 ZMYND11 114610 DIP2C 674189 4 ZMYND11 112815 DIP2C 672394 peak_overlap 0 False 1 False 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (4542891, 38) DONE Done Annotating