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/rosmap/encode_2024/K562_bias/encode_2024.LV.fibroblast.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rosmap/encode_2024/K562_bias/encode_2024.LV.fibroblast.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.fibroblast.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/rosmap/encode_2024/K562_bias/encode_2024.LV.fibroblast.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rosmap/encode_2024/K562_bias/encode_2024.LV.fibroblast.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.fibroblast.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 837619 chr1 850506 850507 A T chr1:850507:A:T 837620 chr1 850562 850563 G C chr1:850563:G:C 837621 chr1 850855 850856 C T chr1:850856:C:T 837622 chr1 851095 851096 G A chr1:851096:G:A 837623 chr1 852046 852047 C T chr1:852047:C:T Variants table shape: (2531122, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 \ 0 chr1 850506 850507 A T chr1:850507:A:T chr1 923923 923924 SAMD11 1 chr1 850506 850507 A T chr1:850507:A:T chr1 959308 959309 NOC2L 2 chr1 850506 850507 A T chr1:850507:A:T chr1 960584 960585 KLHL17 3 chr1 850562 850563 G C chr1:850563:G:C chr1 923923 923924 SAMD11 4 chr1 850562 850563 G C chr1:850563:G:C chr1 959308 959309 NOC2L 10 11 12 13 14 0 0 + ENSG00000187634.13 protein_coding 73417 1 0 - ENSG00000188976.11 protein_coding 108802 2 0 + ENSG00000187961.15 protein_coding 110078 3 0 + ENSG00000187634.13 protein_coding 73361 4 0 - ENSG00000188976.11 protein_coding 108746 Closest genes table shape: (7593366, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 858636 858637 C T chr1:858637:C:T 1 chr1 858749 858750 G A chr1:858750:G:A 2 chr1 869815 869816 A G chr1:869816:A:G 3 chr1 869950 869951 A G chr1:869951:A:G 4 chr1 923768 923769 G A chr1:923769:G:A Peak overlap table shape: (116359, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr10 124524 T A chr10:124524:T:A -0.001313 1 chr10 124526 T A chr10:124526:T:A 0.000791 2 chr10 124528 T A chr10:124528:T:A 0.000960 3 chr10 124530 T A chr10:124530:T:A 0.001371 4 chr10 124542 T A chr10:124542:T:A -0.001133 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.736097 0.013357 0.741682 0.015873 ... 1 0.802406 0.009570 0.809657 0.016549 ... 2 0.881384 0.005847 0.878981 0.016139 ... 3 0.855435 0.006557 0.863334 0.015346 ... 4 0.916650 0.004242 0.915810 0.012227 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.723247 0.000425 1 0.761677 0.000292 2 0.818207 0.000175 3 0.807902 0.000242 4 0.845899 0.000153 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.729596 ZMYND11 5565 1 0.768875 ZMYND11 5563 2 0.814689 ZMYND11 5561 3 0.814141 ZMYND11 5559 4 0.839631 ZMYND11 5547 closest_gene_2 gene_distance_2 closest_gene_3 gene_distance_3 \ 0 TUBB8 50361 DIP2C 565144 1 TUBB8 50363 DIP2C 565142 2 TUBB8 50365 DIP2C 565140 3 TUBB8 50367 DIP2C 565138 4 TUBB8 50379 DIP2C 565126 peak_overlap 0 False 1 False 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (2531122, 38) DONE Done Annotating