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.pericyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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/rare/encode_2024/K562_bias/encode_2024.LV.pericyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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 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: (178823, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 10394 A T chr10:10394:A:T 0.012974 0.556812 1 chr10 10418 A C chr10:10418:A:C -0.008007 0.676484 2 chr10 10532 G A chr10:10532:G:A 0.013424 0.625701 3 chr10 10573 G A chr10:10573:G:A -0.023813 0.514238 4 chr10 10663 G C chr10:10663:G:C 0.030927 0.421107 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.019422 0.568108 0.008051 ... 1 0.013699 0.664084 0.008763 ... 2 0.014932 0.639356 0.006392 ... 3 0.023813 0.496579 0.008097 ... 4 0.030927 0.436870 0.017574 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.127743 1 0.154383 2 0.166591 3 0.110481 4 0.058410 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 0.000110 1 0.000100 2 0.000075 3 0.000170 4 0.000528 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.131292 TUBB8 1 0.149892 TUBB8 2 0.171341 TUBB8 3 0.105591 TUBB8 4 0.061111 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