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/ldsc/encode_2024/K562_bias/encode_2024.LV.macrophage.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/ldsc/encode_2024/K562_bias/encode_2024.LV.macrophage.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.macrophage.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/ldsc/encode_2024/K562_bias/encode_2024.LV.macrophage.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/ldsc/encode_2024/K562_bias/encode_2024.LV.macrophage.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.macrophage.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 1620045 chr1 11007 11008 G C chr1:11008:G:C 1620046 chr1 11011 11012 G C chr1:11012:G:C 1620047 chr1 13109 13110 A G chr1:13110:A:G 1620048 chr1 13115 13116 G T chr1:13116:G:T 1620049 chr1 13117 13118 G A chr1:13118:G:A Variants table shape: (4542891, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 10 \ 0 chr1 11007 11008 G C chr1:11008:G:C chr1 65419 65420 OR4F5 0 1 chr1 11007 11008 G C chr1:11008:G:C chr1 451677 451678 OR4F29 0 2 chr1 11007 11008 G C chr1:11008:G:C chr1 686653 686654 OR4F16 0 3 chr1 11011 11012 G C chr1:11012:G:C chr1 65419 65420 OR4F5 0 4 chr1 11011 11012 G C chr1:11012:G:C chr1 451677 451678 OR4F29 0 11 12 13 14 0 + ENSG00000186092.7 protein_coding 54412 1 - ENSG00000284733.2 protein_coding 440670 2 - ENSG00000284662.2 protein_coding 675646 3 + ENSG00000186092.7 protein_coding 54408 4 - ENSG00000284733.2 protein_coding 440666 Closest genes table shape: (13628673, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 778638 778639 G A chr1:778639:G:A 1 chr1 807213 807214 T C chr1:807214:T:C 2 chr1 807432 807433 T C chr1:807433:T:C 3 chr1 807691 807692 C A chr1:807692:C:A 4 chr1 808039 808040 A G chr1:808040:A:G Peak overlap table shape: (79410, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 14744 C A chr10:14744:C:A -0.017599 0.453396 1 chr10 15391 G A chr10:15391:G:A -0.052341 0.152715 2 chr10 15394 A G chr10:15394:A:G 0.025748 0.358648 3 chr10 15479 A G chr10:15479:A:G -0.015207 0.493953 4 chr10 17274 C G chr10:17274:C:G -0.002621 0.679107 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.017599 0.482050 0.007644 ... 1 0.052341 0.164851 0.012027 ... 2 0.025748 0.336715 0.015392 ... 3 0.017819 0.505442 0.012933 ... 4 0.008262 0.680250 0.009330 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.877065 0.000011 1 0.713512 0.000069 2 0.873847 0.000028 3 0.856732 0.000023 4 0.623220 0.000172 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.893742 TUBB8 59419 1 0.744501 TUBB8 58772 2 0.839255 TUBB8 58769 3 0.865994 TUBB8 58684 4 0.621207 TUBB8 56889 closest_gene_2 gene_distance_2 closest_gene_3 gene_distance_3 \ 0 ZMYND11 115345 DIP2C 674924 1 ZMYND11 114698 DIP2C 674277 2 ZMYND11 114695 DIP2C 674274 3 ZMYND11 114610 DIP2C 674189 4 ZMYND11 112815 DIP2C 672394 peak_overlap 0 False 1 False 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (4542891, 38) DONE Done Annotating