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.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/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/chd/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/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 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 2049922 2049923 G T chr1:2049923:G:T 2 chr1 2894678 2894679 G C chr1:2894679:G:C 3 chr1 2980382 2980383 G A chr1:2980383:G:A 4 chr1 3384558 3384559 A C chr1:3384559:A:C Peak overlap table shape: (1140, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr10 49256 G A chr10:49256:G:A -0.004356 1 chr10 82202 C T chr10:82202:C:T -0.020220 2 chr10 84013 G A chr10:84013:G:A -0.026946 3 chr10 103330 C G chr10:103330:C:G 0.039378 4 chr10 137595 T C chr10:137595:T:C 0.012542 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.651348 0.006946 0.619503 0.009165 ... 1 0.304760 0.020220 0.266699 0.010137 ... 2 0.230104 0.026946 0.200821 0.013746 ... 3 0.084653 0.039378 0.102021 0.016603 ... 4 0.376924 0.012542 0.430069 0.009171 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.853272 0.000673 1 0.321136 0.005137 2 0.268529 0.006220 3 0.139062 0.008026 4 0.316083 0.003977 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.827580 TUBB8 24907 1 0.282760 TUBB8 8039 2 0.236435 TUBB8 9850 3 0.163375 ZMYND11 26759 4 0.363232 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