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.childhood.OPC.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.childhood.OPC', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.childhood.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.childhood.OPC.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/credible/roussos_2024/K562_bias/roussos_2024.childhood.OPC', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/roussos_2024/peaks/overlap/roussos_2024.childhood.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 2443318 2443319 A G rs4648844 2 chr1 2444404 2444405 T G rs6687012 3 chr1 8385299 8385300 C T rs3765971 4 chr1 8408217 8408218 A G rs301792 Peak overlap table shape: (977, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr1 2226509 T C rs1692580 -0.002720 0.832027 1 chr1 2232129 C T rs263533 -0.051027 0.246948 2 chr1 2232677 T C rs263532 0.013225 0.572069 3 chr1 2233496 G T rs263531 -0.008501 0.739567 4 chr1 2235710 C T rs262680 -0.009240 0.597664 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.005815 0.830479 0.007940 ... 1 0.051027 0.242129 0.012865 ... 2 0.016909 0.578070 0.008128 ... 3 0.009701 0.734255 0.010525 ... 4 0.015947 0.592499 0.016024 ... quantile_change.mean.pval abs_quantile_change.mean \ 0 0.491171 0.001928 1 0.192343 0.008656 2 0.392054 0.002672 3 0.420937 0.002594 4 0.285930 0.005343 abs_quantile_change.mean.pval closest_gene_1 gene_distance_1 \ 0 0.488716 SKI 880 1 0.186711 SKI 4740 2 0.397673 SKI 5288 3 0.415701 SKI 6107 4 0.281991 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