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/common/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/common/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.lymphocyte.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/common/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/common/encode_2024/K562_bias/encode_2024.LV.lymphocyte.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.lymphocyte.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 2339836 chr1 10176 10177 A C chr1:10177:A:C 2339837 chr1 10246 10247 T C chr1:10247:T:C 2339838 chr1 10247 10248 A T chr1:10248:A:T 2339839 chr1 10249 10250 A C chr1:10250:A:C 2339840 chr1 10256 10257 A C chr1:10257:A:C Variants table shape: (6565133, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 10 \ 0 chr1 10176 10177 A C chr1:10177:A:C chr1 65419 65420 OR4F5 0 1 chr1 10176 10177 A C chr1:10177:A:C chr1 451677 451678 OR4F29 0 2 chr1 10176 10177 A C chr1:10177:A:C chr1 686653 686654 OR4F16 0 3 chr1 10246 10247 T C chr1:10247:T:C chr1 65419 65420 OR4F5 0 4 chr1 10246 10247 T C chr1:10247:T:C chr1 451677 451678 OR4F29 0 11 12 13 14 0 + ENSG00000186092.7 protein_coding 55243 1 - ENSG00000284733.2 protein_coding 441501 2 - ENSG00000284662.2 protein_coding 676477 3 + ENSG00000186092.7 protein_coding 55173 4 - ENSG00000284733.2 protein_coding 441431 Closest genes table shape: (19695399, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 181021 181022 C T chr1:181022:C:T 1 chr1 181112 181113 A G chr1:181113:A:G 2 chr1 779046 779047 G A chr1:779047:G:A 3 chr1 794298 794299 C G chr1:794299:C:G 4 chr1 827251 827252 T A chr1:827252:T:A Peak overlap table shape: (31395, 6) chr pos allele1 allele2 variant_id logfc.mean logfc.mean.pval \ 0 chr10 10425 A C chr10:10425:A:C -0.004096 0.691101 1 chr10 10559 G A chr10:10559:G:A -0.029807 0.165440 2 chr10 10904 C G chr10:10904:C:G -0.041647 0.097548 3 chr10 10980 G C chr10:10980:G:C 0.045037 0.074225 4 chr10 10982 G A chr10:10982:G:A -0.044970 0.085617 abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.005783 0.679980 0.005112 ... 1 0.029807 0.158048 0.011798 ... 2 0.041647 0.092995 0.012619 ... 3 0.045037 0.078008 0.009986 ... 4 0.044970 0.081527 0.013551 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.519076 1 0.083025 2 0.048038 3 0.049621 4 0.043279 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 0.000018 1 0.000253 2 0.000457 3 0.000399 4 0.000551 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.509564 TUBB8 1 0.078996 TUBB8 2 0.045586 TUBB8 3 0.052259 TUBB8 4 0.041107 TUBB8 gene_distance_1 closest_gene_2 gene_distance_2 closest_gene_3 \ 0 63738 ZMYND11 119664 DIP2C 1 63604 ZMYND11 119530 DIP2C 2 63259 ZMYND11 119185 DIP2C 3 63183 ZMYND11 119109 DIP2C 4 63181 ZMYND11 119107 DIP2C gene_distance_3 peak_overlap 0 679243 False 1 679109 False 2 678764 False 3 678688 False 4 678686 False [5 rows x 34 columns] Annotation table shape: (6565133, 34) DONE Done Annotating