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/chd/encode_2024/K562_bias/encode_2024.LV.endothelial_cell.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.endothelial_cell.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.endothelial_cell.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/chd/encode_2024/K562_bias/encode_2024.LV.endothelial_cell.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.endothelial_cell.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.endothelial_cell.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 56293 chr1 823487 823488 A G chr1:823488:A:G 56294 chr1 843979 843980 A G chr1:843980:A:G 56295 chr1 874954 874955 G A chr1:874955:G:A 56296 chr1 891706 891707 A T chr1:891707:A:T 56297 chr1 898174 898175 C T chr1:898175:C:T Variants table shape: (164181, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 \ 0 chr1 823487 823488 A G chr1:823488:A:G chr1 923923 923924 SAMD11 1 chr1 823487 823488 A G chr1:823488:A:G chr1 959308 959309 NOC2L 2 chr1 823487 823488 A G chr1:823488:A:G chr1 686653 686654 OR4F16 3 chr1 843979 843980 A G chr1:843980:A:G chr1 923923 923924 SAMD11 4 chr1 843979 843980 A G chr1:843980:A:G chr1 959308 959309 NOC2L 10 11 12 13 14 0 0 + ENSG00000187634.13 protein_coding 100436 1 0 - ENSG00000188976.11 protein_coding 135821 2 0 - ENSG00000284662.2 protein_coding 136834 3 0 + ENSG00000187634.13 protein_coding 79944 4 0 - ENSG00000188976.11 protein_coding 115329 Closest genes table shape: (492543, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 1032180 1032181 C T chr1:1032181:C:T 1 chr1 1133328 1133329 A G chr1:1133329:A:G 2 chr1 1133366 1133367 C T chr1:1133367:C:T 3 chr1 1201166 1201167 C A chr1:1201167:C:A 4 chr1 1496299 1496300 C A chr1:1496300:C:A Peak overlap table shape: (3384, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr10 49256 G A chr10:49256:G:A -0.008694 1 chr10 82202 C T chr10:82202:C:T -0.016252 2 chr10 84013 G A chr10:84013:G:A -0.082054 3 chr10 103330 C G chr10:103330:C:G 0.021399 4 chr10 137595 T C chr10:137595:T:C 0.010878 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.438618 0.024534 0.436651 0.013292 ... 1 0.563585 0.017108 0.544810 0.009532 ... 2 0.134577 0.082054 0.126085 0.017150 ... 3 0.476711 0.021399 0.501120 0.009108 ... 4 0.659220 0.010878 0.686516 0.008896 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.155668 0.006615 1 0.386794 0.002090 2 0.158005 0.007700 3 0.231198 0.003610 4 0.738442 0.000142 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.154669 TUBB8 24907 1 0.371987 TUBB8 8039 2 0.146225 TUBB8 9850 3 0.248586 ZMYND11 26759 4 0.765776 ZMYND11 7506 closest_gene_2 gene_distance_2 closest_gene_3 gene_distance_3 \ 0 ZMYND11 80833 DIP2C 640412 1 ZMYND11 47887 DIP2C 607466 2 ZMYND11 46076 DIP2C 605655 3 TUBB8 29167 DIP2C 586338 4 TUBB8 63432 DIP2C 552073 peak_overlap 0 False 1 False 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (164181, 38) DONE Done Annotating