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.neuronal.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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/rare/encode_2024/K562_bias/encode_2024.LV.neuronal.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/rare/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 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 778768 778769 T C chr1:778769:T:C 1 chr1 795186 795187 A C chr1:795187:A:C 2 chr1 817504 817505 G C chr1:817505:G:C 3 chr1 827116 827117 G C chr1:827117:G:C 4 chr1 827509 827510 C T chr1:827510:C:T Peak overlap table shape: (111223, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 10394 A T chr10:10394:A:T 0.000449 0.889760 1 chr10 10418 A C chr10:10418:A:C -0.011772 0.631939 2 chr10 10532 G A chr10:10532:G:A 0.001255 0.546560 3 chr10 10573 G A chr10:10573:G:A -0.022254 0.422862 4 chr10 10663 G C chr10:10663:G:C 0.026184 0.325180 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.002667 0.893130 0.004744 ... 1 0.011772 0.598771 0.007115 ... 2 0.014449 0.539869 0.006413 ... 3 0.022254 0.396594 0.007409 ... 4 0.026184 0.348042 0.013170 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.590049 1 0.296851 2 0.253530 3 0.185187 4 0.094890 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 0.000009 1 0.000057 2 0.000071 3 0.000129 4 0.000282 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.592692 TUBB8 1 0.276300 TUBB8 2 0.248496 TUBB8 3 0.171873 TUBB8 4 0.102649 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