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.pericyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.pericyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.pericyte.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.pericyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/chd/encode_2024/K562_bias/encode_2024.LV.pericyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.pericyte.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 1133328 1133329 A G chr1:1133329:A:G 1 chr1 1133366 1133367 C T chr1:1133367:C:T 2 chr1 1201166 1201167 C A chr1:1201167:C:A 3 chr1 1616194 1616195 G A chr1:1616195:G:A 4 chr1 1862031 1862032 A C chr1:1862032:A:C Peak overlap table shape: (3579, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr10 49256 G A chr10:49256:G:A 0.019981 1 chr10 82202 C T chr10:82202:C:T -0.072975 2 chr10 84013 G A chr10:84013:G:A -0.018273 3 chr10 103330 C G chr10:103330:C:G 0.047136 4 chr10 137595 T C chr10:137595:T:C 0.023821 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.440891 0.031332 0.450203 0.016417 ... 1 0.204551 0.072975 0.193754 0.013871 ... 2 0.527490 0.023876 0.516952 0.012105 ... 3 0.289448 0.047136 0.306073 0.011834 ... 4 0.495038 0.023821 0.516899 0.009424 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.179190 0.007036 1 0.314385 0.002769 2 0.654497 0.000344 3 0.235696 0.004193 4 0.523700 0.000604 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.184900 TUBB8 24907 1 0.298359 TUBB8 8039 2 0.645638 TUBB8 9850 3 0.249721 ZMYND11 26759 4 0.544928 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