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/asd/encode_2024/K562_bias/encode_2024.LV.endocardial.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/encode_2024/K562_bias/encode_2024.LV.endocardial.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.endocardial.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/asd/encode_2024/K562_bias/encode_2024.LV.endocardial.H.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/encode_2024/K562_bias/encode_2024.LV.endocardial.H', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/encode_2024/peaks/overlap/encode_2024.LV.endocardial.H.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 44909 chr1 843979 843980 A G chr1:843980:A:G 1968 chr1 848166 848167 A G chr1:848167:A:G 1969 chr1 894776 894777 A G chr1:894777:A:G 44237 chr1 915678 915679 G A chr1:915679:G:A 1544 chr1 932169 932170 C G chr1:932170:C:G Variants table shape: (84980, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 \ 0 chr1 843979 843980 A G chr1:843980:A:G chr1 923923 923924 SAMD11 1 chr1 843979 843980 A G chr1:843980:A:G chr1 959308 959309 NOC2L 2 chr1 843979 843980 A G chr1:843980:A:G chr1 960584 960585 KLHL17 3 chr1 848166 848167 A G chr1:848167:A:G chr1 923923 923924 SAMD11 4 chr1 848166 848167 A G chr1:848167:A:G chr1 959308 959309 NOC2L 10 11 12 13 14 0 0 + ENSG00000187634.13 protein_coding 79944 1 0 - ENSG00000188976.11 protein_coding 115329 2 0 + ENSG00000187961.15 protein_coding 116605 3 0 + ENSG00000187634.13 protein_coding 75757 4 0 - ENSG00000188976.11 protein_coding 111142 Closest genes table shape: (254940, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 1616194 1616195 G A chr1:1616195:G:A 1 chr1 2279142 2279143 C G chr1:2279143:C:G 2 chr1 2301556 2301557 C T chr1:2301557:C:T 3 chr1 3423357 3423358 C G chr1:3423358:C:G 4 chr1 3619307 3619308 C A chr1:3619308:C:A Peak overlap table shape: (2035, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr1 3747728 T C chr1:3747728:T:C -0.002115 1 chr1 117942118 T G chr1:117942118:T:G 0.001591 2 chr1 163337297 C A chr1:163337297:C:A -0.009165 3 chr1 32951474 G C chr1:32951474:G:C 0.027797 4 chr1 214496189 G C chr1:214496189:G:C -0.005994 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.688302 0.007204 0.689236 0.007962 ... 1 0.862819 0.002801 0.862899 0.006319 ... 2 0.625642 0.009165 0.625921 0.010158 ... 3 0.289806 0.027797 0.292198 0.027873 ... 4 0.677735 0.007888 0.677997 0.007516 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.307374 1 0.765176 2 0.754791 3 0.644297 4 0.547013 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 0.000036 1 0.000001 2 0.000001 3 0.000003 4 0.000007 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.306204 CCDC27 1 0.765696 WDR3 2 0.755379 RGS5 3 0.645789 RNF19B 4 0.544930 PTPN14 gene_distance_1 closest_gene_2 gene_distance_2 closest_gene_3 \ 0 1267 SMIM1 25022 LRRC47 1 12397 GDAP2 12497 SPAG17 2 15506 NUF2 70720 RGS4 3 13335 TMEM54 50036 HPCA 4 56260 CENPF 106997 SMYD2 gene_distance_3 peak_overlap 0 48770 False 1 243110 False 2 268521 False 3 65479 False 4 215086 False [5 rows x 34 columns] Annotation table shape: (84980, 34) DONE Done Annotating