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.neuronal.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.neuronal.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.neuronal.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.neuronal.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.neuronal.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.neuronal.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 1616194 1616195 G A chr1:1616195:G:A 1 chr1 2315453 2315454 C T chr1:2315454:C:T 2 chr1 2969035 2969036 T C chr1:2969036:T:C 3 chr1 3171260 3171261 C T chr1:3171261:C:T 4 chr1 3424692 3424693 G C chr1:3424693:G:C Peak overlap table shape: (2265, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr10 49256 G A chr10:49256:G:A -0.019219 1 chr10 82202 C T chr10:82202:C:T 0.017276 2 chr10 84013 G A chr10:84013:G:A -0.060614 3 chr10 103330 C G chr10:103330:C:G 0.021174 4 chr10 137595 T C chr10:137595:T:C 0.020097 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.494321 0.019219 0.460654 0.013480 ... 1 0.387929 0.027529 0.396639 0.016184 ... 2 0.157128 0.062154 0.148679 0.019113 ... 3 0.379739 0.021174 0.414006 0.010649 ... 4 0.395292 0.020097 0.429424 0.015504 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.364348 0.005160 1 0.302466 0.005864 2 0.416066 0.004021 3 0.404509 0.003093 4 0.737659 0.000513 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.335265 TUBB8 24907 1 0.311752 TUBB8 8039 2 0.389708 TUBB8 9850 3 0.441937 ZMYND11 26759 4 0.782780 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