join_jansen_and_kunkle_tables.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "jansen_data = pd.read_csv(\"/home/eramamur/resources/gwas/AD_sumstats_Jansenetal.txt\",sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "kunkle_data = pd.read_csv(\"/home/eramamur/resources/gwas/Kunkle_etal_Stage1_results.txt\", sep=' ')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>uniqID.a1a2</th>\n",
       "      <th>CHR</th>\n",
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       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>SNP</th>\n",
       "      <th>Z</th>\n",
       "      <th>P</th>\n",
       "      <th>Nsum</th>\n",
       "      <th>Neff</th>\n",
       "      <th>dir</th>\n",
       "      <th>MAF</th>\n",
       "      <th>BETA</th>\n",
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       "      <td>G</td>\n",
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      ],
      "text/plain": [
       "    uniqID.a1a2  CHR      BP A1 A2          SNP         Z        P    Nsum  \\\n",
       "0  1:715265_T_C    1  715265  T  C   rs12184267  2.121973  0.03384  381761   \n",
       "1  1:715367_G_A    1  715367  G  A   rs12184277  1.957915  0.05024  382151   \n",
       "2  1:717485_A_C    1  717485  A  C   rs12184279  1.912438  0.05582  382180   \n",
       "3  1:720381_T_G    1  720381  T  G  rs116801199  2.295404  0.02171  382954   \n",
       "4  1:721290_C_G    1  721290  C  G   rs12565286  2.315602  0.02058  382779   \n",
       "\n",
       "       Neff   dir       MAF      BETA        SE  \n",
       "0  381761.0  ??+?  0.040807  0.012275  0.005785  \n",
       "1  382151.0  ??+?  0.041069  0.011285  0.005764  \n",
       "2  382180.0  ??+?  0.040576  0.011087  0.005797  \n",
       "3  382954.0  ??+?  0.042162  0.013052  0.005686  \n",
       "4  382779.0  ??+?  0.042378  0.013137  0.005673  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_data.join(kunkle_data, on)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Chromosome</th>\n",
       "      <th>Position</th>\n",
       "      <th>MarkerName</th>\n",
       "      <th>Effect_allele</th>\n",
       "      <th>Non_Effect_allele</th>\n",
       "      <th>Beta</th>\n",
       "      <th>SE</th>\n",
       "      <th>Pvalue</th>\n",
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       "      <td>T</td>\n",
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       "      <td>1</td>\n",
       "      <td>100000989</td>\n",
       "      <td>chr1:100000989:I</td>\n",
       "      <td>A</td>\n",
       "      <td>ATC</td>\n",
       "      <td>-0.0099</td>\n",
       "      <td>0.0343</td>\n",
       "      <td>0.7731</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
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       "      <td>rs144406489</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0061</td>\n",
       "      <td>0.0612</td>\n",
       "      <td>0.9204</td>\n",
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      ],
      "text/plain": [
       "   Chromosome   Position        MarkerName Effect_allele Non_Effect_allele  \\\n",
       "0           1  100000012        rs10875231             T                 G   \n",
       "1           1  100000827         rs6678176             T                 C   \n",
       "2           1  100000843        rs78286437             T                 C   \n",
       "3           1  100000989  chr1:100000989:I             A               ATC   \n",
       "4           1  100001138       rs144406489             A                 G   \n",
       "\n",
       "     Beta      SE  Pvalue  \n",
       "0 -0.0026  0.0168  0.8758  \n",
       "1  0.0008  0.0156  0.9574  \n",
       "2 -0.0136  0.0330  0.6792  \n",
       "3 -0.0099  0.0343  0.7731  \n",
       "4 -0.0061  0.0612  0.9204  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "kunkle_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "jansen_kunkle_data_merged = pd.merge(jansen_data,\n",
    "         kunkle_data,\n",
    "         how='outer',\n",
    "         left_on=\"SNP\",\n",
    "         right_on=\"MarkerName\",\n",
    "         suffixes=[\"Jansen\", \"Kunkle\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(15550367, 22)"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_names = jansen_kunkle_data_merged.loc[~jansen_kunkle_data_merged[\"MarkerName\"].isnull() | ~jansen_kunkle_data_merged[\"SNP\"].isnull()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(15548080, 22)"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_names.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(6249794, 22)"
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_names[jansen_kunkle_data_merged_snps_with_valid_names[\"SNP\"].isnull()|jansen_kunkle_data_merged_snps_with_valid_names[\"MarkerName\"].isnull()].shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_and_matching_names = jansen_kunkle_data_merged_snps_with_valid_names.loc[jansen_kunkle_data_merged_snps_with_valid_names[\"SNP\"]==jansen_kunkle_data_merged_snps_with_valid_names[\"MarkerName\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(9298286, 22)"
      ]
     },
     "execution_count": 73,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_and_matching_names.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>uniqID.a1a2</th>\n",
       "      <th>CHR</th>\n",
       "      <th>BP</th>\n",
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       "      <th>Effect_allele</th>\n",
       "      <th>Non_Effect_allele</th>\n",
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       "      <td>0.001870</td>\n",
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       "      <td>13.0</td>\n",
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       "      <td>0.987699</td>\n",
       "      <td>0.323300</td>\n",
       "      <td>386548.0</td>\n",
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       "      <td>0.012903</td>\n",
       "      <td>0.013064</td>\n",
       "      <td>4.0</td>\n",
       "      <td>150102520.0</td>\n",
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       "      <td>T</td>\n",
       "      <td>C</td>\n",
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       "      <td>3:58792675_T_C</td>\n",
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       "      <td>T</td>\n",
       "      <td>rs9814616</td>\n",
       "      <td>-2.165623</td>\n",
       "      <td>0.030340</td>\n",
       "      <td>387076.0</td>\n",
       "      <td>387076.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.066531</td>\n",
       "      <td>0.030722</td>\n",
       "      <td>12.0</td>\n",
       "      <td>74005158.0</td>\n",
       "      <td>rs9814616</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0258</td>\n",
       "      <td>0.0172</td>\n",
       "      <td>0.133900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3678009</th>\n",
       "      <td>4:106694621_T_C</td>\n",
       "      <td>4.0</td>\n",
       "      <td>106694621.0</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>rs111881411</td>\n",
       "      <td>1.562522</td>\n",
       "      <td>0.118165</td>\n",
       "      <td>458117.0</td>\n",
       "      <td>451388.66</td>\n",
       "      <td>...</td>\n",
       "      <td>0.003828</td>\n",
       "      <td>0.002450</td>\n",
       "      <td>12.0</td>\n",
       "      <td>65374658.0</td>\n",
       "      <td>rs111881411</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1883</td>\n",
       "      <td>0.2109</td>\n",
       "      <td>0.371800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3973673</th>\n",
       "      <td>4:166492912_T_C</td>\n",
       "      <td>4.0</td>\n",
       "      <td>166492912.0</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>rs111612834</td>\n",
       "      <td>-0.588048</td>\n",
       "      <td>0.556500</td>\n",
       "      <td>386982.0</td>\n",
       "      <td>386982.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.008014</td>\n",
       "      <td>0.013628</td>\n",
       "      <td>11.0</td>\n",
       "      <td>109116370.0</td>\n",
       "      <td>rs111612834</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1977</td>\n",
       "      <td>0.1972</td>\n",
       "      <td>0.316000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4513453</th>\n",
       "      <td>5:85091480_A_G</td>\n",
       "      <td>5.0</td>\n",
       "      <td>85091480.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs78201962</td>\n",
       "      <td>-0.587006</td>\n",
       "      <td>0.557200</td>\n",
       "      <td>387076.0</td>\n",
       "      <td>387076.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.010731</td>\n",
       "      <td>0.018280</td>\n",
       "      <td>1.0</td>\n",
       "      <td>196664874.0</td>\n",
       "      <td>rs78201962</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0832</td>\n",
       "      <td>0.0810</td>\n",
       "      <td>0.304300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5031931</th>\n",
       "      <td>6:9693761_C_T</td>\n",
       "      <td>6.0</td>\n",
       "      <td>9693761.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>rs77280639</td>\n",
       "      <td>1.195493</td>\n",
       "      <td>0.231894</td>\n",
       "      <td>458144.0</td>\n",
       "      <td>451415.42</td>\n",
       "      <td>...</td>\n",
       "      <td>0.006578</td>\n",
       "      <td>0.005502</td>\n",
       "      <td>10.0</td>\n",
       "      <td>128104527.0</td>\n",
       "      <td>rs77280639</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1137</td>\n",
       "      <td>0.2942</td>\n",
       "      <td>0.699200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5172950</th>\n",
       "      <td>6:31324691_A_G</td>\n",
       "      <td>6.0</td>\n",
       "      <td>31324691.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs3177891</td>\n",
       "      <td>-0.838055</td>\n",
       "      <td>0.402000</td>\n",
       "      <td>387077.0</td>\n",
       "      <td>387077.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.031614</td>\n",
       "      <td>0.037724</td>\n",
       "      <td>6.0</td>\n",
       "      <td>31239602.0</td>\n",
       "      <td>rs3177891</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0227</td>\n",
       "      <td>0.0443</td>\n",
       "      <td>0.609000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5195822</th>\n",
       "      <td>6:32630717_C_A</td>\n",
       "      <td>6.0</td>\n",
       "      <td>32630717.0</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>rs17613542</td>\n",
       "      <td>1.039225</td>\n",
       "      <td>0.298700</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.015048</td>\n",
       "      <td>0.014480</td>\n",
       "      <td>6.0</td>\n",
       "      <td>32630660.0</td>\n",
       "      <td>rs17613542</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0246</td>\n",
       "      <td>0.0223</td>\n",
       "      <td>0.270100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5195876</th>\n",
       "      <td>6:32631086_G_A</td>\n",
       "      <td>6.0</td>\n",
       "      <td>32631086.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs58770498</td>\n",
       "      <td>0.463090</td>\n",
       "      <td>0.643300</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.011885</td>\n",
       "      <td>0.025665</td>\n",
       "      <td>6.0</td>\n",
       "      <td>32631029.0</td>\n",
       "      <td>rs58770498</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.0380</td>\n",
       "      <td>0.639100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6253520</th>\n",
       "      <td>7:67690493_A_G</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67690493.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs3113154</td>\n",
       "      <td>0.653242</td>\n",
       "      <td>0.513600</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.008568</td>\n",
       "      <td>0.013116</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67690495.0</td>\n",
       "      <td>rs3113154</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0056</td>\n",
       "      <td>0.0165</td>\n",
       "      <td>0.732800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6254262</th>\n",
       "      <td>7:67782758_C_G</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67782758.0</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>rs3113049</td>\n",
       "      <td>-0.676064</td>\n",
       "      <td>0.499000</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.018506</td>\n",
       "      <td>0.027374</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67782757.0</td>\n",
       "      <td>rs3113049</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0385</td>\n",
       "      <td>0.0393</td>\n",
       "      <td>0.327800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6254305</th>\n",
       "      <td>7:67790555_G_A</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67790555.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs12534993</td>\n",
       "      <td>-1.437415</td>\n",
       "      <td>0.150600</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.016229</td>\n",
       "      <td>0.011291</td>\n",
       "      <td>7.0</td>\n",
       "      <td>67790557.0</td>\n",
       "      <td>rs12534993</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0559</td>\n",
       "      <td>0.0597</td>\n",
       "      <td>0.349100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6699494</th>\n",
       "      <td>8:2329093_G_A</td>\n",
       "      <td>8.0</td>\n",
       "      <td>2329093.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs10110406</td>\n",
       "      <td>-0.421760</td>\n",
       "      <td>0.673200</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.005199</td>\n",
       "      <td>0.012328</td>\n",
       "      <td>8.0</td>\n",
       "      <td>2284841.0</td>\n",
       "      <td>rs10110406</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0053</td>\n",
       "      <td>0.0201</td>\n",
       "      <td>0.793700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9495351</th>\n",
       "      <td>12:27227134_A_G</td>\n",
       "      <td>12.0</td>\n",
       "      <td>27227134.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs61920386</td>\n",
       "      <td>-0.316127</td>\n",
       "      <td>0.751906</td>\n",
       "      <td>458641.0</td>\n",
       "      <td>451908.09</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.001019</td>\n",
       "      <td>0.003222</td>\n",
       "      <td>11.0</td>\n",
       "      <td>10970520.0</td>\n",
       "      <td>rs61920386</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0736</td>\n",
       "      <td>0.1086</td>\n",
       "      <td>0.497900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9723265</th>\n",
       "      <td>12:76569784_G_C</td>\n",
       "      <td>12.0</td>\n",
       "      <td>76569784.0</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>rs5016153</td>\n",
       "      <td>0.013536</td>\n",
       "      <td>0.989200</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000155</td>\n",
       "      <td>0.011428</td>\n",
       "      <td>12.0</td>\n",
       "      <td>76569788.0</td>\n",
       "      <td>rs5016153</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0080</td>\n",
       "      <td>0.0203</td>\n",
       "      <td>0.693900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9743060</th>\n",
       "      <td>12:81181814_G_A</td>\n",
       "      <td>12.0</td>\n",
       "      <td>81181814.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs76577941</td>\n",
       "      <td>-0.534349</td>\n",
       "      <td>0.593100</td>\n",
       "      <td>386533.0</td>\n",
       "      <td>386533.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.005479</td>\n",
       "      <td>0.010254</td>\n",
       "      <td>13.0</td>\n",
       "      <td>36891367.0</td>\n",
       "      <td>rs76577941</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0908</td>\n",
       "      <td>0.0830</td>\n",
       "      <td>0.274200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10161958</th>\n",
       "      <td>13:52861210_C_A</td>\n",
       "      <td>13.0</td>\n",
       "      <td>52861210.0</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>rs2760812</td>\n",
       "      <td>-0.024317</td>\n",
       "      <td>0.980600</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.000610</td>\n",
       "      <td>0.025094</td>\n",
       "      <td>13.0</td>\n",
       "      <td>53099680.0</td>\n",
       "      <td>rs2760812</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.1223</td>\n",
       "      <td>0.0660</td>\n",
       "      <td>0.064020</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11446562</th>\n",
       "      <td>16:35190354_C_G</td>\n",
       "      <td>16.0</td>\n",
       "      <td>35190354.0</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>rs11859869</td>\n",
       "      <td>1.675838</td>\n",
       "      <td>0.093770</td>\n",
       "      <td>386999.0</td>\n",
       "      <td>386999.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.022963</td>\n",
       "      <td>0.013702</td>\n",
       "      <td>11.0</td>\n",
       "      <td>61962672.0</td>\n",
       "      <td>rs11859869</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0868</td>\n",
       "      <td>0.0748</td>\n",
       "      <td>0.246000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11485477</th>\n",
       "      <td>16:55866287_A_G</td>\n",
       "      <td>16.0</td>\n",
       "      <td>55866287.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs7188256</td>\n",
       "      <td>-1.647964</td>\n",
       "      <td>0.099360</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.041350</td>\n",
       "      <td>0.025092</td>\n",
       "      <td>16.0</td>\n",
       "      <td>55795236.0</td>\n",
       "      <td>rs7188256</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0208</td>\n",
       "      <td>0.0217</td>\n",
       "      <td>0.337500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11975439</th>\n",
       "      <td>17:67366931_C_T</td>\n",
       "      <td>17.0</td>\n",
       "      <td>67366931.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>rs2586556</td>\n",
       "      <td>1.478403</td>\n",
       "      <td>0.139300</td>\n",
       "      <td>54162.0</td>\n",
       "      <td>54162.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.048100</td>\n",
       "      <td>0.032500</td>\n",
       "      <td>17.0</td>\n",
       "      <td>67366925.0</td>\n",
       "      <td>rs2586556</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0342</td>\n",
       "      <td>0.0354</td>\n",
       "      <td>0.334200</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13196747</th>\n",
       "      <td>22:18462550_D_I</td>\n",
       "      <td>22.0</td>\n",
       "      <td>18462550.0</td>\n",
       "      <td>D</td>\n",
       "      <td>I</td>\n",
       "      <td>rs58179741</td>\n",
       "      <td>-1.819797</td>\n",
       "      <td>0.068790</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.021891</td>\n",
       "      <td>0.012029</td>\n",
       "      <td>22.0</td>\n",
       "      <td>18462560.0</td>\n",
       "      <td>rs58179741</td>\n",
       "      <td>CA</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0385</td>\n",
       "      <td>0.0875</td>\n",
       "      <td>0.659900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13198094</th>\n",
       "      <td>22:18889969_G_A</td>\n",
       "      <td>22.0</td>\n",
       "      <td>18889969.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs2904549</td>\n",
       "      <td>1.253291</td>\n",
       "      <td>0.210100</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.019087</td>\n",
       "      <td>0.015230</td>\n",
       "      <td>22.0</td>\n",
       "      <td>18889968.0</td>\n",
       "      <td>rs2904549</td>\n",
       "      <td>A</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>0.0288</td>\n",
       "      <td>0.750000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13238794</th>\n",
       "      <td>22:27436973_T_A</td>\n",
       "      <td>22.0</td>\n",
       "      <td>27436973.0</td>\n",
       "      <td>T</td>\n",
       "      <td>A</td>\n",
       "      <td>rs12159421</td>\n",
       "      <td>-1.095266</td>\n",
       "      <td>0.273400</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.015523</td>\n",
       "      <td>0.014173</td>\n",
       "      <td>22.0</td>\n",
       "      <td>27436972.0</td>\n",
       "      <td>rs12159421</td>\n",
       "      <td>A</td>\n",
       "      <td>AT</td>\n",
       "      <td>-0.0126</td>\n",
       "      <td>0.0162</td>\n",
       "      <td>0.434800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13266026</th>\n",
       "      <td>22:32822891_G_A</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32822891.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs5749434</td>\n",
       "      <td>0.818976</td>\n",
       "      <td>0.412800</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.011505</td>\n",
       "      <td>0.014048</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32822890.0</td>\n",
       "      <td>rs5749434</td>\n",
       "      <td>A</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.0119</td>\n",
       "      <td>0.0144</td>\n",
       "      <td>0.410100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13282150</th>\n",
       "      <td>22:35548923_G_T</td>\n",
       "      <td>22.0</td>\n",
       "      <td>35548923.0</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>rs2413303</td>\n",
       "      <td>-0.141215</td>\n",
       "      <td>0.887700</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.001680</td>\n",
       "      <td>0.011896</td>\n",
       "      <td>22.0</td>\n",
       "      <td>35548922.0</td>\n",
       "      <td>rs2413303</td>\n",
       "      <td>G</td>\n",
       "      <td>GATAT</td>\n",
       "      <td>-0.0250</td>\n",
       "      <td>0.0159</td>\n",
       "      <td>0.116400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13294661</th>\n",
       "      <td>22:37995102_C_T</td>\n",
       "      <td>22.0</td>\n",
       "      <td>37995102.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>rs6519075</td>\n",
       "      <td>-1.088442</td>\n",
       "      <td>0.276400</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.011771</td>\n",
       "      <td>0.010815</td>\n",
       "      <td>22.0</td>\n",
       "      <td>37995101.0</td>\n",
       "      <td>rs6519075</td>\n",
       "      <td>T</td>\n",
       "      <td>TC</td>\n",
       "      <td>-0.0027</td>\n",
       "      <td>0.0146</td>\n",
       "      <td>0.854700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13305379</th>\n",
       "      <td>22:40667996_A_G</td>\n",
       "      <td>22.0</td>\n",
       "      <td>40667996.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs880379</td>\n",
       "      <td>-0.436464</td>\n",
       "      <td>0.662500</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.005462</td>\n",
       "      <td>0.012513</td>\n",
       "      <td>22.0</td>\n",
       "      <td>40667994.0</td>\n",
       "      <td>rs880379</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>-0.0348</td>\n",
       "      <td>0.0169</td>\n",
       "      <td>0.039170</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13312469</th>\n",
       "      <td>22:42386057_G_T</td>\n",
       "      <td>22.0</td>\n",
       "      <td>42386057.0</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>rs133297</td>\n",
       "      <td>1.158157</td>\n",
       "      <td>0.246800</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.014332</td>\n",
       "      <td>0.012375</td>\n",
       "      <td>22.0</td>\n",
       "      <td>42386056.0</td>\n",
       "      <td>rs133297</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>-0.0048</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.787600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13342232</th>\n",
       "      <td>22:47418459_C_A</td>\n",
       "      <td>22.0</td>\n",
       "      <td>47418459.0</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>rs8138096</td>\n",
       "      <td>0.266181</td>\n",
       "      <td>0.790100</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.003081</td>\n",
       "      <td>0.011574</td>\n",
       "      <td>22.0</td>\n",
       "      <td>47418458.0</td>\n",
       "      <td>rs8138096</td>\n",
       "      <td>A</td>\n",
       "      <td>AC</td>\n",
       "      <td>0.0070</td>\n",
       "      <td>0.0162</td>\n",
       "      <td>0.664900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13351860</th>\n",
       "      <td>22:49058298_D_I</td>\n",
       "      <td>22.0</td>\n",
       "      <td>49058298.0</td>\n",
       "      <td>D</td>\n",
       "      <td>I</td>\n",
       "      <td>rs61576921</td>\n",
       "      <td>-0.518370</td>\n",
       "      <td>0.604200</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.006414</td>\n",
       "      <td>0.012372</td>\n",
       "      <td>22.0</td>\n",
       "      <td>49058299.0</td>\n",
       "      <td>rs61576921</td>\n",
       "      <td>G</td>\n",
       "      <td>GGTGATTC</td>\n",
       "      <td>0.0160</td>\n",
       "      <td>0.0166</td>\n",
       "      <td>0.335000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>34 rows × 22 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              uniqID.a1a2   CHR           BP A1 A2          SNP         Z  \\\n",
       "364922     1:81711991_T_C   1.0   81711991.0  T  C   rs12035877  0.510016   \n",
       "386418     1:86180643_A_G   1.0   86180643.0  A  G  rs111453363  0.204338   \n",
       "1531098   2:105570695_A_G   2.0  105570695.0  A  G  rs111528057  0.987699   \n",
       "2098152   2:230258379_C_T   2.0  230258379.0  C  T  rs111432249  2.538905   \n",
       "2467823    3:58792675_T_C   3.0   58792675.0  T  C  rs111532776  0.560859   \n",
       "2479627    3:60946574_G_T   3.0   60946574.0  G  T    rs9814616 -2.165623   \n",
       "3678009   4:106694621_T_C   4.0  106694621.0  T  C  rs111881411  1.562522   \n",
       "3973673   4:166492912_T_C   4.0  166492912.0  T  C  rs111612834 -0.588048   \n",
       "4513453    5:85091480_A_G   5.0   85091480.0  A  G   rs78201962 -0.587006   \n",
       "5031931     6:9693761_C_T   6.0    9693761.0  C  T   rs77280639  1.195493   \n",
       "5172950    6:31324691_A_G   6.0   31324691.0  A  G    rs3177891 -0.838055   \n",
       "5195822    6:32630717_C_A   6.0   32630717.0  C  A   rs17613542  1.039225   \n",
       "5195876    6:32631086_G_A   6.0   32631086.0  G  A   rs58770498  0.463090   \n",
       "6253520    7:67690493_A_G   7.0   67690493.0  A  G    rs3113154  0.653242   \n",
       "6254262    7:67782758_C_G   7.0   67782758.0  C  G    rs3113049 -0.676064   \n",
       "6254305    7:67790555_G_A   7.0   67790555.0  G  A   rs12534993 -1.437415   \n",
       "6699494     8:2329093_G_A   8.0    2329093.0  G  A   rs10110406 -0.421760   \n",
       "9495351   12:27227134_A_G  12.0   27227134.0  A  G   rs61920386 -0.316127   \n",
       "9723265   12:76569784_G_C  12.0   76569784.0  G  C    rs5016153  0.013536   \n",
       "9743060   12:81181814_G_A  12.0   81181814.0  G  A   rs76577941 -0.534349   \n",
       "10161958  13:52861210_C_A  13.0   52861210.0  C  A    rs2760812 -0.024317   \n",
       "11446562  16:35190354_C_G  16.0   35190354.0  C  G   rs11859869  1.675838   \n",
       "11485477  16:55866287_A_G  16.0   55866287.0  A  G    rs7188256 -1.647964   \n",
       "11975439  17:67366931_C_T  17.0   67366931.0  C  T    rs2586556  1.478403   \n",
       "13196747  22:18462550_D_I  22.0   18462550.0  D  I   rs58179741 -1.819797   \n",
       "13198094  22:18889969_G_A  22.0   18889969.0  G  A    rs2904549  1.253291   \n",
       "13238794  22:27436973_T_A  22.0   27436973.0  T  A   rs12159421 -1.095266   \n",
       "13266026  22:32822891_G_A  22.0   32822891.0  G  A    rs5749434  0.818976   \n",
       "13282150  22:35548923_G_T  22.0   35548923.0  G  T    rs2413303 -0.141215   \n",
       "13294661  22:37995102_C_T  22.0   37995102.0  C  T    rs6519075 -1.088442   \n",
       "13305379  22:40667996_A_G  22.0   40667996.0  A  G     rs880379 -0.436464   \n",
       "13312469  22:42386057_G_T  22.0   42386057.0  G  T     rs133297  1.158157   \n",
       "13342232  22:47418459_C_A  22.0   47418459.0  C  A    rs8138096  0.266181   \n",
       "13351860  22:49058298_D_I  22.0   49058298.0  D  I   rs61576921 -0.518370   \n",
       "\n",
       "                 P      Nsum       Neff  ...      BETA  SEJansen  Chromosome  \\\n",
       "364922    0.610040  456743.0  450026.66  ...  0.001075  0.002108        12.0   \n",
       "386418    0.838090  456655.0  449939.43  ...  0.001870  0.009154        13.0   \n",
       "1531098   0.323300  386548.0  386548.00  ...  0.012903  0.013064         4.0   \n",
       "2098152   0.011120   17477.0   17477.00  ...  0.048559  0.019126        11.0   \n",
       "2467823   0.574894  458420.0  451689.01  ...  0.002622  0.004674        18.0   \n",
       "2479627   0.030340  387076.0  387076.00  ... -0.066531  0.030722        12.0   \n",
       "3678009   0.118165  458117.0  451388.66  ...  0.003828  0.002450        12.0   \n",
       "3973673   0.556500  386982.0  386982.00  ... -0.008014  0.013628        11.0   \n",
       "4513453   0.557200  387076.0  387076.00  ... -0.010731  0.018280         1.0   \n",
       "5031931   0.231894  458144.0  451415.42  ...  0.006578  0.005502        10.0   \n",
       "5172950   0.402000  387077.0  387077.00  ... -0.031614  0.037724         6.0   \n",
       "5195822   0.298700   17477.0   17477.00  ...  0.015048  0.014480         6.0   \n",
       "5195876   0.643300   17477.0   17477.00  ...  0.011885  0.025665         6.0   \n",
       "6253520   0.513600   17477.0   17477.00  ...  0.008568  0.013116         7.0   \n",
       "6254262   0.499000   17477.0   17477.00  ... -0.018506  0.027374         7.0   \n",
       "6254305   0.150600   17477.0   17477.00  ... -0.016229  0.011291         7.0   \n",
       "6699494   0.673200   17477.0   17477.00  ... -0.005199  0.012328         8.0   \n",
       "9495351   0.751906  458641.0  451908.09  ... -0.001019  0.003222        11.0   \n",
       "9723265   0.989200   17477.0   17477.00  ...  0.000155  0.011428        12.0   \n",
       "9743060   0.593100  386533.0  386533.00  ... -0.005479  0.010254        13.0   \n",
       "10161958  0.980600   17477.0   17477.00  ... -0.000610  0.025094        13.0   \n",
       "11446562  0.093770  386999.0  386999.00  ...  0.022963  0.013702        11.0   \n",
       "11485477  0.099360   17477.0   17477.00  ... -0.041350  0.025092        16.0   \n",
       "11975439  0.139300   54162.0   54162.00  ...  0.048100  0.032500        17.0   \n",
       "13196747  0.068790   17477.0   17477.00  ... -0.021891  0.012029        22.0   \n",
       "13198094  0.210100   17477.0   17477.00  ...  0.019087  0.015230        22.0   \n",
       "13238794  0.273400   17477.0   17477.00  ... -0.015523  0.014173        22.0   \n",
       "13266026  0.412800   17477.0   17477.00  ...  0.011505  0.014048        22.0   \n",
       "13282150  0.887700   17477.0   17477.00  ... -0.001680  0.011896        22.0   \n",
       "13294661  0.276400   17477.0   17477.00  ... -0.011771  0.010815        22.0   \n",
       "13305379  0.662500   17477.0   17477.00  ... -0.005462  0.012513        22.0   \n",
       "13312469  0.246800   17477.0   17477.00  ...  0.014332  0.012375        22.0   \n",
       "13342232  0.790100   17477.0   17477.00  ...  0.003081  0.011574        22.0   \n",
       "13351860  0.604200   17477.0   17477.00  ... -0.006414  0.012372        22.0   \n",
       "\n",
       "             Position   MarkerName  Effect_allele Non_Effect_allele    Beta  \\\n",
       "364922     11619927.0   rs12035877              A                 G  0.1387   \n",
       "386418     67334758.0  rs111453363              T                 C  0.5928   \n",
       "1531098   150102520.0  rs111528057              T                 C  0.1616   \n",
       "2098152   124460969.0  rs111432249              A                 C -0.1424   \n",
       "2467823    31367214.0  rs111532776              C                 G -0.0485   \n",
       "2479627    74005158.0    rs9814616              A                 G -0.0258   \n",
       "3678009    65374658.0  rs111881411              T                 C  0.1883   \n",
       "3973673   109116370.0  rs111612834              T                 C  0.1977   \n",
       "4513453   196664874.0   rs78201962              A                 G -0.0832   \n",
       "5031931   128104527.0   rs77280639              A                 C  0.1137   \n",
       "5172950    31239602.0    rs3177891              A                 G -0.0227   \n",
       "5195822    32630660.0   rs17613542              T                 C  0.0246   \n",
       "5195876    32631029.0   rs58770498              T                 C  0.0178   \n",
       "6253520    67690495.0    rs3113154              A                 G -0.0056   \n",
       "6254262    67782757.0    rs3113049              A                 G -0.0385   \n",
       "6254305    67790557.0   rs12534993              A                 G  0.0559   \n",
       "6699494     2284841.0   rs10110406              T                 C  0.0053   \n",
       "9495351    10970520.0   rs61920386              A                 G  0.0736   \n",
       "9723265    76569788.0    rs5016153              C                 G  0.0080   \n",
       "9743060    36891367.0   rs76577941              T                 C -0.0908   \n",
       "10161958   53099680.0    rs2760812              T                 G  0.1223   \n",
       "11446562   61962672.0   rs11859869              T                 C -0.0868   \n",
       "11485477   55795236.0    rs7188256              T                 C -0.0208   \n",
       "11975439   67366925.0    rs2586556              T                 C -0.0342   \n",
       "13196747   18462560.0   rs58179741             CA                 C -0.0385   \n",
       "13198094   18889968.0    rs2904549              A                AG  0.0092   \n",
       "13238794   27436972.0   rs12159421              A                AT -0.0126   \n",
       "13266026   32822890.0    rs5749434              A                AG  0.0119   \n",
       "13282150   35548922.0    rs2413303              G             GATAT -0.0250   \n",
       "13294661   37995101.0    rs6519075              T                TC -0.0027   \n",
       "13305379   40667994.0     rs880379              T                TG -0.0348   \n",
       "13312469   42386056.0     rs133297              T                TG -0.0048   \n",
       "13342232   47418458.0    rs8138096              A                AC  0.0070   \n",
       "13351860   49058299.0   rs61576921              G          GGTGATTC  0.0160   \n",
       "\n",
       "         SEKunkle    Pvalue  \n",
       "364922     0.0806  0.085320  \n",
       "386418     0.5210  0.255200  \n",
       "1531098    0.0548  0.003174  \n",
       "2098152    0.0814  0.080050  \n",
       "2467823    0.0577  0.399700  \n",
       "2479627    0.0172  0.133900  \n",
       "3678009    0.2109  0.371800  \n",
       "3973673    0.1972  0.316000  \n",
       "4513453    0.0810  0.304300  \n",
       "5031931    0.2942  0.699200  \n",
       "5172950    0.0443  0.609000  \n",
       "5195822    0.0223  0.270100  \n",
       "5195876    0.0380  0.639100  \n",
       "6253520    0.0165  0.732800  \n",
       "6254262    0.0393  0.327800  \n",
       "6254305    0.0597  0.349100  \n",
       "6699494    0.0201  0.793700  \n",
       "9495351    0.1086  0.497900  \n",
       "9723265    0.0203  0.693900  \n",
       "9743060    0.0830  0.274200  \n",
       "10161958   0.0660  0.064020  \n",
       "11446562   0.0748  0.246000  \n",
       "11485477   0.0217  0.337500  \n",
       "11975439   0.0354  0.334200  \n",
       "13196747   0.0875  0.659900  \n",
       "13198094   0.0288  0.750000  \n",
       "13238794   0.0162  0.434800  \n",
       "13266026   0.0144  0.410100  \n",
       "13282150   0.0159  0.116400  \n",
       "13294661   0.0146  0.854700  \n",
       "13305379   0.0169  0.039170  \n",
       "13312469   0.0178  0.787600  \n",
       "13342232   0.0162  0.664900  \n",
       "13351860   0.0166  0.335000  \n",
       "\n",
       "[34 rows x 22 columns]"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_and_matching_names.loc[~(jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"Position\"]==jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"BP\"])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>uniqID.a1a2</th>\n",
       "      <th>CHR</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>SNP</th>\n",
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       "      <td>0.001870</td>\n",
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       "      <td>0.987699</td>\n",
       "      <td>0.323300</td>\n",
       "      <td>386548.0</td>\n",
       "      <td>386548.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.012903</td>\n",
       "      <td>0.013064</td>\n",
       "      <td>4.0</td>\n",
       "      <td>150102520.0</td>\n",
       "      <td>rs111528057</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1616</td>\n",
       "      <td>0.0548</td>\n",
       "      <td>0.003174</td>\n",
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       "    <tr>\n",
       "      <th>2098152</th>\n",
       "      <td>2:230258379_C_T</td>\n",
       "      <td>2.0</td>\n",
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       "      <td>T</td>\n",
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       "      <td>2.538905</td>\n",
       "      <td>0.011120</td>\n",
       "      <td>17477.0</td>\n",
       "      <td>17477.00</td>\n",
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       "      <td>0.048559</td>\n",
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       "      <td>11.0</td>\n",
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       "      <td>rs111432249</td>\n",
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       "      <th>2467823</th>\n",
       "      <td>3:58792675_T_C</td>\n",
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       "      <td>18.0</td>\n",
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       "      <td>T</td>\n",
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       "      <td>458117.0</td>\n",
       "      <td>451388.66</td>\n",
       "      <td>...</td>\n",
       "      <td>0.003828</td>\n",
       "      <td>0.002450</td>\n",
       "      <td>12.0</td>\n",
       "      <td>65374658.0</td>\n",
       "      <td>rs111881411</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1883</td>\n",
       "      <td>0.2109</td>\n",
       "      <td>0.371800</td>\n",
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       "    <tr>\n",
       "      <th>3973673</th>\n",
       "      <td>4:166492912_T_C</td>\n",
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       "      <td>166492912.0</td>\n",
       "      <td>T</td>\n",
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       "      <td>0.556500</td>\n",
       "      <td>386982.0</td>\n",
       "      <td>386982.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.008014</td>\n",
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       "      <td>109116370.0</td>\n",
       "      <td>rs111612834</td>\n",
       "      <td>T</td>\n",
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       "      <th>4513453</th>\n",
       "      <td>5:85091480_A_G</td>\n",
       "      <td>5.0</td>\n",
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       "      <td>387076.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.010731</td>\n",
       "      <td>0.018280</td>\n",
       "      <td>1.0</td>\n",
       "      <td>196664874.0</td>\n",
       "      <td>rs78201962</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>-0.0832</td>\n",
       "      <td>0.0810</td>\n",
       "      <td>0.304300</td>\n",
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       "      <th>5031931</th>\n",
       "      <td>6:9693761_C_T</td>\n",
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       "      <td>9693761.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>rs77280639</td>\n",
       "      <td>1.195493</td>\n",
       "      <td>0.231894</td>\n",
       "      <td>458144.0</td>\n",
       "      <td>451415.42</td>\n",
       "      <td>...</td>\n",
       "      <td>0.006578</td>\n",
       "      <td>0.005502</td>\n",
       "      <td>10.0</td>\n",
       "      <td>128104527.0</td>\n",
       "      <td>rs77280639</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1137</td>\n",
       "      <td>0.2942</td>\n",
       "      <td>0.699200</td>\n",
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       "      <th>9495351</th>\n",
       "      <td>12:27227134_A_G</td>\n",
       "      <td>12.0</td>\n",
       "      <td>27227134.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>rs61920386</td>\n",
       "      <td>-0.316127</td>\n",
       "      <td>0.751906</td>\n",
       "      <td>458641.0</td>\n",
       "      <td>451908.09</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.001019</td>\n",
       "      <td>0.003222</td>\n",
       "      <td>11.0</td>\n",
       "      <td>10970520.0</td>\n",
       "      <td>rs61920386</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0736</td>\n",
       "      <td>0.1086</td>\n",
       "      <td>0.497900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9743060</th>\n",
       "      <td>12:81181814_G_A</td>\n",
       "      <td>12.0</td>\n",
       "      <td>81181814.0</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>rs76577941</td>\n",
       "      <td>-0.534349</td>\n",
       "      <td>0.593100</td>\n",
       "      <td>386533.0</td>\n",
       "      <td>386533.00</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.005479</td>\n",
       "      <td>0.010254</td>\n",
       "      <td>13.0</td>\n",
       "      <td>36891367.0</td>\n",
       "      <td>rs76577941</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0908</td>\n",
       "      <td>0.0830</td>\n",
       "      <td>0.274200</td>\n",
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       "    <tr>\n",
       "      <th>11446562</th>\n",
       "      <td>16:35190354_C_G</td>\n",
       "      <td>16.0</td>\n",
       "      <td>35190354.0</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>rs11859869</td>\n",
       "      <td>1.675838</td>\n",
       "      <td>0.093770</td>\n",
       "      <td>386999.0</td>\n",
       "      <td>386999.00</td>\n",
       "      <td>...</td>\n",
       "      <td>0.022963</td>\n",
       "      <td>0.013702</td>\n",
       "      <td>11.0</td>\n",
       "      <td>61962672.0</td>\n",
       "      <td>rs11859869</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>-0.0868</td>\n",
       "      <td>0.0748</td>\n",
       "      <td>0.246000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13 rows × 22 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              uniqID.a1a2   CHR           BP A1 A2          SNP         Z  \\\n",
       "364922     1:81711991_T_C   1.0   81711991.0  T  C   rs12035877  0.510016   \n",
       "386418     1:86180643_A_G   1.0   86180643.0  A  G  rs111453363  0.204338   \n",
       "1531098   2:105570695_A_G   2.0  105570695.0  A  G  rs111528057  0.987699   \n",
       "2098152   2:230258379_C_T   2.0  230258379.0  C  T  rs111432249  2.538905   \n",
       "2467823    3:58792675_T_C   3.0   58792675.0  T  C  rs111532776  0.560859   \n",
       "2479627    3:60946574_G_T   3.0   60946574.0  G  T    rs9814616 -2.165623   \n",
       "3678009   4:106694621_T_C   4.0  106694621.0  T  C  rs111881411  1.562522   \n",
       "3973673   4:166492912_T_C   4.0  166492912.0  T  C  rs111612834 -0.588048   \n",
       "4513453    5:85091480_A_G   5.0   85091480.0  A  G   rs78201962 -0.587006   \n",
       "5031931     6:9693761_C_T   6.0    9693761.0  C  T   rs77280639  1.195493   \n",
       "9495351   12:27227134_A_G  12.0   27227134.0  A  G   rs61920386 -0.316127   \n",
       "9743060   12:81181814_G_A  12.0   81181814.0  G  A   rs76577941 -0.534349   \n",
       "11446562  16:35190354_C_G  16.0   35190354.0  C  G   rs11859869  1.675838   \n",
       "\n",
       "                 P      Nsum       Neff  ...      BETA  SEJansen  Chromosome  \\\n",
       "364922    0.610040  456743.0  450026.66  ...  0.001075  0.002108        12.0   \n",
       "386418    0.838090  456655.0  449939.43  ...  0.001870  0.009154        13.0   \n",
       "1531098   0.323300  386548.0  386548.00  ...  0.012903  0.013064         4.0   \n",
       "2098152   0.011120   17477.0   17477.00  ...  0.048559  0.019126        11.0   \n",
       "2467823   0.574894  458420.0  451689.01  ...  0.002622  0.004674        18.0   \n",
       "2479627   0.030340  387076.0  387076.00  ... -0.066531  0.030722        12.0   \n",
       "3678009   0.118165  458117.0  451388.66  ...  0.003828  0.002450        12.0   \n",
       "3973673   0.556500  386982.0  386982.00  ... -0.008014  0.013628        11.0   \n",
       "4513453   0.557200  387076.0  387076.00  ... -0.010731  0.018280         1.0   \n",
       "5031931   0.231894  458144.0  451415.42  ...  0.006578  0.005502        10.0   \n",
       "9495351   0.751906  458641.0  451908.09  ... -0.001019  0.003222        11.0   \n",
       "9743060   0.593100  386533.0  386533.00  ... -0.005479  0.010254        13.0   \n",
       "11446562  0.093770  386999.0  386999.00  ...  0.022963  0.013702        11.0   \n",
       "\n",
       "             Position   MarkerName  Effect_allele Non_Effect_allele    Beta  \\\n",
       "364922     11619927.0   rs12035877              A                 G  0.1387   \n",
       "386418     67334758.0  rs111453363              T                 C  0.5928   \n",
       "1531098   150102520.0  rs111528057              T                 C  0.1616   \n",
       "2098152   124460969.0  rs111432249              A                 C -0.1424   \n",
       "2467823    31367214.0  rs111532776              C                 G -0.0485   \n",
       "2479627    74005158.0    rs9814616              A                 G -0.0258   \n",
       "3678009    65374658.0  rs111881411              T                 C  0.1883   \n",
       "3973673   109116370.0  rs111612834              T                 C  0.1977   \n",
       "4513453   196664874.0   rs78201962              A                 G -0.0832   \n",
       "5031931   128104527.0   rs77280639              A                 C  0.1137   \n",
       "9495351    10970520.0   rs61920386              A                 G  0.0736   \n",
       "9743060    36891367.0   rs76577941              T                 C -0.0908   \n",
       "11446562   61962672.0   rs11859869              T                 C -0.0868   \n",
       "\n",
       "         SEKunkle    Pvalue  \n",
       "364922     0.0806  0.085320  \n",
       "386418     0.5210  0.255200  \n",
       "1531098    0.0548  0.003174  \n",
       "2098152    0.0814  0.080050  \n",
       "2467823    0.0577  0.399700  \n",
       "2479627    0.0172  0.133900  \n",
       "3678009    0.2109  0.371800  \n",
       "3973673    0.1972  0.316000  \n",
       "4513453    0.0810  0.304300  \n",
       "5031931    0.2942  0.699200  \n",
       "9495351    0.1086  0.497900  \n",
       "9743060    0.0830  0.274200  \n",
       "11446562   0.0748  0.246000  \n",
       "\n",
       "[13 rows x 22 columns]"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_and_matching_names.loc[~(jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"Position\"]==jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"BP\"]) & ~(jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"Chromosome\"]==jansen_kunkle_data_merged_snps_with_valid_and_matching_names[\"CHR\"])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "15548080"
      ]
     },
     "execution_count": 74,
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   "source": [
    "9298286+6249794"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(15548080, 22)"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
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   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(6249794, 22)"
      ]
     },
     "execution_count": 67,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_names.loc[jansen_kunkle_data_merged_snps_with_valid_names[\"SNP\"].isnull() | jansen_kunkle_data_merged_snps_with_valid_names[\"MarkerName\"].isnull()].shape"
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  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(6249794, 22)"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "(jansen_kunkle_data_merged_snps_with_valid_names.loc[~(jansen_kunkle_data_merged_snps_with_valid_names[\"SNP\"]==jansen_kunkle_data_merged_snps_with_valid_names[\"MarkerName\"])]).shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0, 22)"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jansen_kunkle_data_merged_snps_with_valid_names.loc[jansen_kunkle_data_merged_snps_with_valid_names[\"SNP\"].isnull() & jansen_kunkle_data_merged_snps_with_valid_names[\"MarkerName\"].isnull()].shape"
   ]
  }
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