diff --git a/code/association_scan/quantile_twas/quantile_twas.ipynb b/code/association_scan/quantile_twas/quantile_twas.ipynb
index 96812828..fe892f4e 100644
--- a/code/association_scan/quantile_twas/quantile_twas.ipynb
+++ b/code/association_scan/quantile_twas/quantile_twas.ipynb
@@ -761,8 +761,10 @@
     "        qr_results = quantile_twas_weight_pipeline(X = X, \n",
     "                                            Y = Y, \n",
     "                                            Z = Z, \n",
-    "                                            maf = NULL, #only use for LD pruning, it will calculate MAF automatically\n",
-    "                                            extract_region_name = extract_region_name[[r]],\n",
+    "                                            ld_reference_meta_file=${('\"%s\"' % ld_reference_meta_file) if not ld_reference_meta_file.is_dir() else \"NULL\"},\n",
+    "                                            maf = fdat$maf[[r]],\n",
+    "                                            maf_cutoff = 0.01,                                            \n",
+    "                                            region_id = extract_region_name[[r]],\n",
     "                                            quantile_qtl_tau_list = seq(0.05, 0.95, 0.05),\n",
     "                                            quantile_twas_tau_list = seq(0.01, 0.99, by = 0.01))\n",
     "\n",
@@ -785,7 +787,8 @@
     "        if (!is.null(qr_results$message)) {\n",
     "            message(qr_results$message)\n",
     "        }\n",
-    "            \n",
+    "        \n",
+    "        fitted[[r]]$region_info = region_info    \n",
     "        condition_names <- c(condition_names, new_names)\n",
     "            \n",
     "        # Release memory\n",