diff --git a/code/association_scan/quantile_models/qr_and_twas.ipynb b/code/association_scan/quantile_models/qr_and_twas.ipynb
index 077369b76..d4ba9f4e9 100644
--- a/code/association_scan/quantile_models/qr_and_twas.ipynb
+++ b/code/association_scan/quantile_models/qr_and_twas.ipynb
@@ -125,7 +125,7 @@
     "\n",
     "\n",
     "\n",
-    "Additionally, the matrix of quantile TWAS weights and pseudo R-squares is calculated and saved using Koenker and Machado's Pseudo R\u00b2 method, as described in their [Koenker and Machado, 1999: Inference in Quantile Regression](https://www.maths.usyd.edu.au/u/jchan/GLM/Koenker&Machado1999InferenceQuantileReg.pdf)"
+    "Additionally, the matrix of quantile TWAS weights and pseudo R-squares is calculated and saved using Koenker and Machado's Pseudo R² method, as described in their [Koenker and Machado, 1999: Inference in Quantile Regression](https://www.maths.usyd.edu.au/u/jchan/GLM/Koenker&Machado1999InferenceQuantileReg.pdf)"
    ]
   },
   {
@@ -356,13 +356,18 @@
     "parameter: indel = True\n",
     "parameter: min_twas_maf = 0.01\n",
     "parameter: screen_threshold = 0.01\n",
-    "parameter: qrank_screen_calculate = True\n",
-    "parameter: marginal_beta_calculate = True\n",
-    "parameter: twas_weight_calculate = True\n",
-    "parameter: vqtl_calculate = True\n",
+    "parameter: screen_method = \"qvalue\"\n",
+    "parameter: screen_significant = True\n",
+    "parameter: pre_filter_by_pqr = False\n",
+    "parameter: initial_corr_filter_cutoff = 0.8\n",
+    "parameter: full_rank_corr_filter_cutoff = \"seq(0.75, 0.5, by = -0.05)\"\n",
     "parameter: ld_reference_meta_file = path()\n",
     "# Only focus on a subset of variants\n",
     "parameter: keep_variants = path()\n",
+    "parameter: marginal_beta_calculate = True\n",
+    "parameter: twas_weight_calculate = True\n",
+    "parameter: qrank_screen_calculate = True\n",
+    "parameter: vqtl_calculate = True\n",
     "# Analysis environment settings\n",
     "parameter: container = \"\"\n",
     "# For cluster jobs, number commands to run per job\n",
@@ -716,9 +721,11 @@
     "          # Multi-column format: filter by context and molecular_trait_object_id\n",
     "          # For genotype loading: use union of all matching variants across all contexts\n",
     "          current_region = \"${_meta_info[2]}\"\n",
+    "          original_region_ids = c(${\",\".join([(\"'%s'\" % x) if isinstance(x, str) else \",\".join([\"'%s'\" % i for i in x]) for x in _meta_info[3]])})\n",
+    "          all_region_ids = unique(c(current_region, original_region_ids))\n",
     "          current_contexts = conditions\n",
     "          keep_variants_region_data = keep_variants_data[\n",
-    "            keep_variants_data$molecular_trait_object_id == current_region &\n",
+    "            keep_variants_data$molecular_trait_object_id %in% all_region_ids &\n",
     "            keep_variants_data$context %in% current_contexts, ]\n",
     "          keep_variants_list = unique(as.character(keep_variants_region_data$variant_id))\n",
     "          keep_variants_list = keep_variants_list[keep_variants_list != \"\"]\n",
@@ -727,9 +734,7 @@
     "          message(paste(length(keep_variants_list), \"variants matched for region\", current_region,\n",
     "                        \"across\", length(current_contexts), \"contexts (per-context filtering enabled)\"))\n",
     "          if (length(keep_variants_list) == 0) {\n",
-    "            message(\"No matching variants found, proceeding without variant filter\")\n",
-    "            keep_variants_list = NULL\n",
-    "            keep_variants_per_context = FALSE\n",
+    "            message(\"No matching variants found for this region, marginal coef will be skipped for contexts without variants\")\n",
     "          }\n",
     "        } else {\n",
     "          # Fallback: treat first column as variant_id list\n",
@@ -811,8 +816,8 @@
     "                current_keep_variants = current_keep_variants[current_keep_variants != \"\"]\n",
     "                message(paste(length(current_keep_variants), \"variants for context\", ctx_name))\n",
     "              } else {\n",
-    "                current_keep_variants = NULL\n",
-    "                message(paste(\"No context-specific variants for\", ctx_name, \"- no variant filter applied\"))\n",
+    "                current_keep_variants = character(0)\n",
+    "                message(paste(\"No context-specific variants for\", ctx_name, \"- skipping marginal coef fitting\"))\n",
     "              }\n",
     "            }\n",
     "\n",
@@ -826,7 +831,12 @@
     "                region_id = paste0(colnames(Y_col), \"_\", names(fdat$residual_Y)[r]),\n",
     "                quantile_qtl_tau_list = seq(0.05, 0.95, by = 0.05),\n",
     "                quantile_twas_tau_list = seq(0.01, 0.99, by = 0.01),\n",
+    "                screen_method = \"${screen_method}\",\n",
     "                screen_threshold = ${screen_threshold},\n",
+    "                screen_significant = ${\"TRUE\" if screen_significant else \"FALSE\"},\n",
+    "                pre_filter_by_pqr = ${\"TRUE\" if pre_filter_by_pqr else \"FALSE\"},\n",
+    "                initial_corr_filter_cutoff = ${initial_corr_filter_cutoff},\n",
+    "                full_rank_corr_filter_cutoff = ${full_rank_corr_filter_cutoff},\n",
     "                keep_variants = current_keep_variants,\n",
     "                marginal_beta_calculate = ${\"TRUE\" if marginal_beta_calculate else \"FALSE\"},\n",
     "                twas_weight_calculate = ${\"TRUE\" if twas_weight_calculate else \"FALSE\"},\n",
@@ -912,4 +922,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
\ No newline at end of file
+}