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/rare/encode_2024/K562_bias/encode_2024.LV.fibroblast.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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/rare/encode_2024/K562_bias/encode_2024.LV.fibroblast.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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 3230544 chr1 10126 10127 A T chr1:10127:A:T 3230545 chr1 10127 10128 A G chr1:10128:A:G 3230546 chr1 10133 10134 A G chr1:10134:A:G 3230547 chr1 10451 10452 A G chr1:10452:A:G 3230548 chr1 10452 10453 C A chr1:10453:C:A Variants table shape: (9126367, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 10 \ 0 chr1 10126 10127 A T chr1:10127:A:T chr1 65419 65420 OR4F5 0 1 chr1 10126 10127 A T chr1:10127:A:T chr1 451677 451678 OR4F29 0 2 chr1 10126 10127 A T chr1:10127:A:T chr1 686653 686654 OR4F16 0 3 chr1 10127 10128 A G chr1:10128:A:G chr1 65419 65420 OR4F5 0 4 chr1 10127 10128 A G chr1:10128:A:G chr1 451677 451678 OR4F29 0 11 12 13 14 0 + ENSG00000186092.7 protein_coding 55293 1 - ENSG00000284733.2 protein_coding 441551 2 - ENSG00000284662.2 protein_coding 676527 3 + ENSG00000186092.7 protein_coding 55292 4 - ENSG00000284733.2 protein_coding 441550 Closest genes table shape: (27379101, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 10451 10452 A G chr1:10452:A:G 1 chr1 10452 10453 C A chr1:10453:C:A 2 chr1 10456 10457 A G chr1:10457:A:G 3 chr1 10461 10462 T G chr1:10462:T:G 4 chr1 10484 10485 G A chr1:10485:G:A Peak overlap table shape: (302918, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 10394 A T chr10:10394:A:T 0.017865 0.643508 1 chr10 10418 A C chr10:10418:A:C 0.001377 0.831213 2 chr10 10532 G A chr10:10532:G:A 0.015420 0.686937 3 chr10 10573 G A chr10:10573:G:A -0.031038 0.493651 4 chr10 10663 G C chr10:10663:G:C 0.029522 0.474649 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.017865 0.664491 0.006086 ... 1 0.009022 0.821354 0.008021 ... 2 0.015420 0.708179 0.008043 ... 3 0.032956 0.480972 0.009896 ... 4 0.031640 0.488277 0.012852 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.222732 1 0.293407 2 0.178891 3 0.120671 4 0.088987 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 0.000075 1 0.000049 2 0.000097 3 0.000275 4 0.000381 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.234332 TUBB8 1 0.286282 TUBB8 2 0.188762 TUBB8 3 0.116778 TUBB8 4 0.092283 TUBB8 gene_distance_1 closest_gene_2 gene_distance_2 closest_gene_3 \ 0 63769 ZMYND11 119695 DIP2C 1 63745 ZMYND11 119671 DIP2C 2 63631 ZMYND11 119557 DIP2C 3 63590 ZMYND11 119516 DIP2C 4 63500 ZMYND11 119426 DIP2C gene_distance_3 peak_overlap 0 679274 False 1 679250 False 2 679136 False 3 679095 False 4 679005 False [5 rows x 34 columns] Annotation table shape: (9126367, 34) DONE Done Annotating