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.adulthood.OPC.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.adulthood.OPC', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.adulthood.OPC.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.adulthood.OPC.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.adulthood.OPC', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.adulthood.OPC.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 2271527 2271528 T C rs903908 1 chr1 2444404 2444405 T G rs6687012 2 chr1 8408217 8408218 A G rs301792 3 chr1 8409276 8409277 A G rs301789 4 chr1 8424167 8424168 C T rs159961 Peak overlap table shape: (673, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr1 2226509 T C rs1692580 0.008783 0.688244 1 chr1 2232129 C T rs263533 -0.050680 0.200621 2 chr1 2232677 T C rs263532 -0.003214 0.752363 3 chr1 2233496 G T rs263531 -0.029087 0.357975 4 chr1 2235710 C T rs262680 -0.010928 0.256265 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.008783 0.695590 0.007160 ... 1 0.050680 0.195711 0.013512 ... 2 0.007305 0.747883 0.007206 ... 3 0.029087 0.350338 0.009352 ... 4 0.040020 0.252513 0.017916 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.500490 0.002647 1 0.145699 0.012410 2 0.667812 0.001360 3 0.203569 0.008866 4 0.118292 0.013810 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.508092 SKI 880 1 0.141599 SKI 4740 2 0.664229 SKI 5288 3 0.197767 SKI 6107 4 0.115649 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 False 2 False 3 False 4 False [5 rows x 38 columns] Annotation table shape: (26215, 38) DONE Done Annotating