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/credible/roussos_2024/K562_bias/roussos_2024.adolescence.GABA.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.adolescence.GABA', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.adolescence.GABA.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/credible/roussos_2024/K562_bias/roussos_2024.adolescence.GABA.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.adolescence.GABA', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.adolescence.GABA.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 0 chr1 2226508 2226509 T C rs1692580 1 chr1 2232128 2232129 C T rs263533 2 chr1 2232676 2232677 T C rs263532 3 chr1 2233495 2233496 G T rs263531 4 chr1 2235709 2235710 C T rs262680 Variants table shape: (26215, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 \ 0 chr1 2226508 2226509 T C rs1692580 chr1 2227388 2227389 SKI 1 chr1 2226508 2226509 T C rs1692580 chr1 2212719 2212720 FAAP20 2 chr1 2226508 2226509 T C rs1692580 chr1 2391706 2391707 MORN1 3 chr1 2232128 2232129 C T rs263533 chr1 2227388 2227389 SKI 4 chr1 2232128 2232129 C T rs263533 chr1 2212719 2212720 FAAP20 10 11 12 13 14 0 0 + ENSG00000157933.11 protein_coding 880 1 0 - ENSG00000162585.17 protein_coding 13789 2 0 - ENSG00000116151.14 protein_coding 165198 3 0 + ENSG00000157933.11 protein_coding 4740 4 0 - ENSG00000162585.17 protein_coding 19409 Closest genes table shape: (78645, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 2232128 2232129 C T rs263533 1 chr1 2444404 2444405 T G rs6687012 2 chr1 2450128 2450129 A G rs867810 3 chr1 2461208 2461209 G C rs2477686 4 chr1 8409276 8409277 A G rs301789 Peak overlap table shape: (743, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr1 2226509 T C rs1692580 0.011721 0.555025 1 chr1 2232129 C T rs263533 -0.076398 0.046126 2 chr1 2232677 T C rs263532 0.007257 0.659445 3 chr1 2233496 G T rs263531 -0.019338 0.426291 4 chr1 2235710 C T rs262680 -0.018066 0.445456 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.011721 0.567637 0.009201 ... 1 0.076398 0.044901 0.015067 ... 2 0.008366 0.669123 0.007298 ... 3 0.019338 0.415693 0.011092 ... 4 0.018066 0.434445 0.019727 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.324571 0.003963 1 0.106270 0.012513 2 0.562777 0.001414 3 0.319318 0.004425 4 0.228599 0.006887 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.336399 SKI 880 1 0.100980 SKI 4740 2 0.573513 SKI 5288 3 0.307870 SKI 6107 4 0.219093 SKI 8321 closest_gene_2 gene_distance_2 closest_gene_3 gene_distance_3 \ 0 FAAP20 13789 MORN1 165198 1 FAAP20 19409 MORN1 159578 2 FAAP20 19957 MORN1 159030 3 FAAP20 20776 MORN1 158211 4 FAAP20 22990 MORN1 155997 peak_overlap 0 False 1 True 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (26215, 38) DONE Done Annotating