ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgaGACGAGUCU--UGAUGUGAg 5' || |||| | ||||||| Target 5' tgcCTACTCACATTTCTACACTt 3'	899 - 921	156.00	-14.50
2	miRNA 3' cgAGAC-GAGUCUUGAUGUGAg 5' | || || : |||||:|:| Target 5' caTATGACTGGAAACTATATTc 3'	169 - 190	127.00	-11.90
3	miRNA 3' cgagacgAGUCU---UGAUGUGAg 5' ||||| |||| ||| Target 5' ggagaagTCAGACTCACTAGACTt 3'	76 - 99	126.00	-10.70

Mutant ID	Mutant Position	Mutant Source
COSN27535818	8	COSMIC
COSN30466566	19	COSMIC
COSN27001030	28	COSMIC
COSN30515021	36	COSMIC
COSN30153966	52	COSMIC
COSN31508618	90	COSMIC
COSN7242432	358	COSMIC
COSN1833537	761	COSMIC
COSN21916363	1743	COSMIC
COSN19568328	2142	COSMIC
COSN18986561	2493	COSMIC
COSN26298689	2644	COSMIC
COSN7242437	2886	COSMIC
COSN17975065	3858	COSMIC
COSN17122444	3879	COSMIC
COSN20628213	3902	COSMIC
COSN16756045	4899	COSMIC
COSN15371036	4935	COSMIC
rs72781665	350	GWAS
rs72781667	2931	GWAS
rs113362373	4621	GWAS
rs7422667	4744	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1158153972	1	dbSNP
rs747095744	1	dbSNP
rs371072453	2	dbSNP
rs1195047902	3	dbSNP
rs776345312	7	dbSNP
rs768756879	8	dbSNP
rs761387092	21	dbSNP
rs1467309539	23	dbSNP
rs764758491	26	dbSNP
rs1438045631	31	dbSNP
rs890695301	36	dbSNP
rs772774991	37	dbSNP
rs762603745	45	dbSNP
rs781412631	45	dbSNP
rs766100627	50	dbSNP
rs751342826	53	dbSNP
rs1462233068	68	dbSNP
rs1243249145	86	dbSNP
rs10186915	91	dbSNP
rs1159617851	96	dbSNP
rs1323419647	97	dbSNP
rs1254818459	98	dbSNP
rs878946800	99	dbSNP
rs1230062201	102	dbSNP
rs1211605243	107	dbSNP
rs762902922	108	dbSNP
rs1295050585	112	dbSNP
rs543592686	116	dbSNP
rs1005080641	118	dbSNP
rs1385312054	128	dbSNP
rs1337446301	133	dbSNP
rs140758090	149	dbSNP
rs1399978317	152	dbSNP
rs757766899	166	dbSNP
rs1482998120	167	dbSNP
rs1166292952	172	dbSNP
rs1446046253	178	dbSNP
rs1385528185	179	dbSNP
rs911438707	187	dbSNP
rs942904875	193	dbSNP
rs1254359043	196	dbSNP
rs1473131773	197	dbSNP
rs145877496	198	dbSNP
rs3088337	206	dbSNP
rs1226711074	217	dbSNP
rs149482799	225	dbSNP
rs369003723	225	dbSNP
rs1316079583	226	dbSNP
rs1245256426	230	dbSNP
rs1338793073	231	dbSNP
rs1435179734	243	dbSNP
rs577603833	249	dbSNP
rs1395730648	259	dbSNP
rs1024258583	267	dbSNP
rs1041744278	268	dbSNP
rs1428971149	274	dbSNP
rs1426375635	279	dbSNP
rs1385465692	284	dbSNP
rs1306117963	287	dbSNP
rs1295401059	288	dbSNP
rs72851398	293	dbSNP
rs1365054838	297	dbSNP
rs1184550870	305	dbSNP
rs1420182056	311	dbSNP
rs1251803726	316	dbSNP
rs1410208909	323	dbSNP
rs1203450851	341	dbSNP
rs72781665	350	dbSNP
rs572618308	362	dbSNP
rs1053734401	371	dbSNP
rs1354294801	383	dbSNP
rs1281318608	386	dbSNP
rs1239926394	387	dbSNP
rs895043035	395	dbSNP
rs1012117274	396	dbSNP
rs1301311150	397	dbSNP
rs767866891	400	dbSNP
rs1302089080	406	dbSNP
rs957131061	411	dbSNP
rs1386734162	414	dbSNP
rs975098793	418	dbSNP
rs1158628006	419	dbSNP
rs1452507819	425	dbSNP
rs11555490	428	dbSNP
rs920931421	429	dbSNP
rs1180662416	431	dbSNP
rs1481594230	433	dbSNP
rs750716743	434	dbSNP
rs574494839	435	dbSNP
rs1286690417	436	dbSNP
rs986859288	443	dbSNP
rs1226762959	444	dbSNP
rs912171160	448	dbSNP
rs1350054423	451	dbSNP
rs185607400	452	dbSNP
rs1225297804	460	dbSNP
rs1483701351	463	dbSNP
rs114494076	466	dbSNP
rs1434103667	467	dbSNP
rs899300050	468	dbSNP
rs1318571105	476	dbSNP
rs1489564026	479	dbSNP
rs747280880	480	dbSNP
rs930719693	483	dbSNP
rs188502671	490	dbSNP
rs1471222888	497	dbSNP
rs1430667348	498	dbSNP
rs984172727	501	dbSNP
rs1018555346	508	dbSNP
rs964636846	509	dbSNP
rs1194187927	511	dbSNP
rs11555491	517	dbSNP
rs764178951	519	dbSNP
rs1170640356	520	dbSNP
rs1205695171	521	dbSNP
rs1324156978	536	dbSNP
rs976926779	537	dbSNP
rs181692169	541	dbSNP
rs562530750	542	dbSNP
rs1270360517	543	dbSNP
rs1429624577	544	dbSNP
rs1362630529	545	dbSNP
rs946184073	546	dbSNP
rs112713129	547	dbSNP
rs1438108579	550	dbSNP
rs1326187923	553	dbSNP
rs1407473519	555	dbSNP
rs1334092888	565	dbSNP
rs551059407	569	dbSNP
rs1032814519	571	dbSNP
rs1299233976	572	dbSNP
rs1185494817	582	dbSNP
rs1343460489	586	dbSNP
rs936046254	592	dbSNP
rs1207961115	595	dbSNP
rs1439295661	602	dbSNP
rs186548401	611	dbSNP
rs114795698	626	dbSNP
rs916542488	627	dbSNP
rs746928792	641	dbSNP
rs1245993504	642	dbSNP
rs1377829862	648	dbSNP
rs1046314645	653	dbSNP
rs906375796	654	dbSNP
rs1222497553	661	dbSNP
rs1028058338	664	dbSNP
rs955282104	665	dbSNP
rs1247633773	669	dbSNP
rs751332713	680	dbSNP
rs993976205	682	dbSNP
rs1165715704	684	dbSNP
rs1248771117	690	dbSNP
rs1445261036	692	dbSNP
rs545977264	712	dbSNP
rs1180231002	715	dbSNP
rs369950166	719	dbSNP
rs116135489	720	dbSNP
rs1406884688	723	dbSNP
rs1204175372	726	dbSNP
rs920846992	727	dbSNP
rs1293424543	736	dbSNP
rs1222801975	738	dbSNP
rs1320552462	742	dbSNP
rs1018354648	749	dbSNP
rs963707869	754	dbSNP
rs1376150055	757	dbSNP
rs1055956816	774	dbSNP
rs894580814	777	dbSNP
rs998400223	779	dbSNP
rs950153911	781	dbSNP
rs1029847190	788	dbSNP
rs371638691	792	dbSNP
rs1282945760	795	dbSNP
rs977547300	802	dbSNP
rs769662722	806	dbSNP
rs1402587595	823	dbSNP
rs1408544233	825	dbSNP
rs926094900	834	dbSNP
rs1471461404	835	dbSNP
rs1229236835	836	dbSNP
rs957685639	836	dbSNP
rs1267949672	838	dbSNP
rs1327307459	840	dbSNP
rs1487942560	850	dbSNP
rs550947147	851	dbSNP
rs1217306552	858	dbSNP
rs1317000948	860	dbSNP
rs775548195	861	dbSNP
rs1441931061	868	dbSNP
rs115354092	873	dbSNP
rs915908401	879	dbSNP
rs996658717	882	dbSNP
rs1028090933	893	dbSNP
rs1432911090	905	dbSNP
rs1389499788	909	dbSNP
rs950005181	910	dbSNP
rs1473764136	914	dbSNP
rs1046363484	924	dbSNP
rs955165552	930	dbSNP
rs577667636	931	dbSNP
rs929822962	939	dbSNP
rs768608318	944	dbSNP
rs1410998675	948	dbSNP
rs774484007	949	dbSNP
rs1176869839	961	dbSNP
rs1432451657	961	dbSNP
rs1264755346	963	dbSNP
rs1187925553	966	dbSNP
rs1485884886	971	dbSNP
rs1005714822	976	dbSNP
rs1206332988	995	dbSNP
rs1327681982	998	dbSNP
rs1039420915	1008	dbSNP
rs1234334340	1014	dbSNP
rs1311991654	1016	dbSNP
rs369295687	1017	dbSNP
rs1216582302	1025	dbSNP
rs1366253138	1031	dbSNP
rs1319948624	1036	dbSNP
rs1433065823	1039	dbSNP
rs973728547	1044	dbSNP
rs1303363018	1048	dbSNP
rs1465316856	1058	dbSNP
rs1413402241	1065	dbSNP
rs1331692283	1067	dbSNP
rs761883933	1068	dbSNP
rs1415984511	1070	dbSNP
rs373667713	1075	dbSNP
rs952254568	1076	dbSNP
rs553867002	1086	dbSNP
rs1186114808	1103	dbSNP
rs967596784	1105	dbSNP
rs572431999	1109	dbSNP
rs1201557732	1116	dbSNP
rs950170101	1119	dbSNP
rs1254600949	1123	dbSNP
rs549641260	1134	dbSNP
rs1280364500	1135	dbSNP
rs1297227030	1144	dbSNP
rs1226188446	1145	dbSNP
rs1344662410	1146	dbSNP
rs773726599	1153	dbSNP
rs1033599147	1155	dbSNP
rs760903787	1156	dbSNP
rs1400041155	1159	dbSNP
rs991998435	1162	dbSNP
rs915971875	1163	dbSNP
rs13021997	1164	dbSNP
rs12989535	1165	dbSNP
rs1369478261	1169	dbSNP
rs1049590635	1170	dbSNP
rs890915524	1174	dbSNP
rs1211534783	1183	dbSNP
rs1368576421	1184	dbSNP
rs542949241	1186	dbSNP
rs774434117	1187	dbSNP
rs1184155100	1188	dbSNP
rs1364002269	1190	dbSNP
rs1483589732	1195	dbSNP
rs1274121073	1204	dbSNP
rs561611773	1206	dbSNP
rs1015795411	1207	dbSNP
rs961104819	1208	dbSNP
rs576820537	1216	dbSNP
rs548312019	1218	dbSNP
rs142696154	1219	dbSNP
rs1309060085	1226	dbSNP
rs952285322	1241	dbSNP
rs551190291	1251	dbSNP
rs551486956	1253	dbSNP
rs941173461	1254	dbSNP
rs1305758819	1260	dbSNP
rs1426133908	1264	dbSNP
rs559869063	1273	dbSNP
rs527326032	1274	dbSNP
rs972011149	1280	dbSNP
rs981625497	1297	dbSNP
rs1473099918	1304	dbSNP
rs933693166	1304	dbSNP
rs924713504	1305	dbSNP
rs1180529704	1309	dbSNP
rs147362845	1310	dbSNP
rs149334108	1312	dbSNP
rs1330709761	1313	dbSNP
rs35785006	1324	dbSNP
rs537751165	1324	dbSNP
rs149646512	1341	dbSNP
rs144320466	1343	dbSNP
rs1286207137	1349	dbSNP
rs113365896	1351	dbSNP
rs1331323387	1352	dbSNP
rs1234843321	1357	dbSNP
rs1384509945	1357	dbSNP
rs1008509389	1379	dbSNP
rs1482064993	1387	dbSNP
rs554288909	1389	dbSNP
rs1458208044	1390	dbSNP
rs1197307958	1410	dbSNP
rs1036846369	1413	dbSNP
rs1157390434	1414	dbSNP
rs1013064982	1432	dbSNP
rs1247446313	1440	dbSNP
rs1450647307	1444	dbSNP
rs1198448403	1448	dbSNP
rs1449893945	1452	dbSNP
rs1249946457	1457	dbSNP
rs896924194	1471	dbSNP
rs1464380215	1473	dbSNP
rs1023081434	1489	dbSNP
rs760474811	1491	dbSNP
rs77782271	1492	dbSNP
rs1011911200	1506	dbSNP
rs13034804	1518	dbSNP
rs536610402	1526	dbSNP
rs1230572210	1528	dbSNP
rs1026320763	1531	dbSNP
rs1454336991	1532	dbSNP
rs950660869	1538	dbSNP
rs1433801422	1540	dbSNP
rs1388458322	1541	dbSNP
rs1319141156	1568	dbSNP
rs983117453	1571	dbSNP
rs555007812	1584	dbSNP
rs567129330	1590	dbSNP
rs1392324978	1592	dbSNP
rs541630930	1592	dbSNP
rs768203260	1592	dbSNP
rs1189294677	1593	dbSNP
rs779960532	1594	dbSNP
rs1432226748	1602	dbSNP
rs1168811765	1603	dbSNP
rs1390491198	1604	dbSNP
rs1385246454	1607	dbSNP
rs1325774559	1609	dbSNP
rs941220280	1611	dbSNP
rs975265932	1613	dbSNP
rs576784431	1619	dbSNP
rs914657834	1620	dbSNP
rs1295556000	1623	dbSNP
rs933746904	1631	dbSNP
rs1226946732	1639	dbSNP
rs1362423729	1646	dbSNP
rs1339941480	1653	dbSNP
rs1229563231	1654	dbSNP
rs775948838	1656	dbSNP
rs879633513	1658	dbSNP
rs1450773099	1659	dbSNP
rs1251629375	1662	dbSNP
rs1333912764	1664	dbSNP
rs1413189949	1668	dbSNP
rs768803474	1678	dbSNP
rs1372570379	1686	dbSNP
rs544141375	1695	dbSNP
rs1355399617	1696	dbSNP
rs1429134901	1697	dbSNP
rs902872130	1708	dbSNP
rs1388435707	1720	dbSNP
rs1183719362	1729	dbSNP
rs934323334	1754	dbSNP
rs1055137045	1757	dbSNP
rs893373361	1762	dbSNP
rs1483919426	1765	dbSNP
rs1037283753	1767	dbSNP
rs1204039696	1780	dbSNP
rs539008489	1784	dbSNP
rs1339679984	1786	dbSNP
rs1187366198	1791	dbSNP
rs1013534098	1795	dbSNP
rs896955394	1796	dbSNP
rs1380530237	1797	dbSNP
rs1284134404	1799	dbSNP
rs1413260947	1799	dbSNP
rs1352739941	1801	dbSNP
rs1023135252	1805	dbSNP
rs559178107	1812	dbSNP
rs894888711	1814	dbSNP
rs1194532838	1815	dbSNP
rs143645786	1818	dbSNP
rs1026373196	1821	dbSNP
rs1161410353	1824	dbSNP
rs950795669	1824	dbSNP
rs984795322	1829	dbSNP
rs1165417927	1830	dbSNP
rs1017299333	1831	dbSNP
rs376987958	1832	dbSNP
rs1031804387	1841	dbSNP
rs544772003	1847	dbSNP
rs1248164919	1854	dbSNP
rs921106412	1855	dbSNP
rs990271729	1856	dbSNP
rs1289731337	1858	dbSNP
rs1021695809	1859	dbSNP
rs1331895167	1861	dbSNP
rs1289359449	1862	dbSNP
rs954134197	1864	dbSNP
rs1208568795	1868	dbSNP
rs146332624	1869	dbSNP
rs1367472179	1882	dbSNP
rs1321710750	1883	dbSNP
rs986533189	1892	dbSNP
rs943962867	1893	dbSNP
rs972638134	1894	dbSNP
rs141999342	1903	dbSNP
rs1242324346	1906	dbSNP
rs931169443	1907	dbSNP
rs868232638	1908	dbSNP
rs934347905	1920	dbSNP
rs1054118404	1921	dbSNP
rs1210108602	1922	dbSNP
rs1466633634	1934	dbSNP
rs1048245982	1937	dbSNP
rs1228106125	1937	dbSNP
rs1335044001	1942	dbSNP
rs1315529357	1946	dbSNP
rs914845244	1949	dbSNP
rs1219999569	1954	dbSNP
rs772166566	1956	dbSNP
rs1044632974	1963	dbSNP
rs907382510	1964	dbSNP
rs1003018151	1965	dbSNP
rs371008512	1967	dbSNP
rs1319827911	1968	dbSNP
rs1451296464	1974	dbSNP
rs886517799	1975	dbSNP
rs1006674182	1985	dbSNP
rs144195260	1986	dbSNP
rs965038065	1988	dbSNP
rs1432214597	1989	dbSNP
rs1256047793	1990	dbSNP
rs1189861707	1997	dbSNP
rs531487921	2000	dbSNP
rs1449557382	2001	dbSNP
rs1422631121	2010	dbSNP
rs1028174588	2015	dbSNP
rs1208680573	2016	dbSNP
rs1485199660	2018	dbSNP
rs766770822	2019	dbSNP
rs955234210	2020	dbSNP
rs549692035	2022	dbSNP
rs1002168302	2026	dbSNP
rs1472360580	2027	dbSNP
rs986580216	2028	dbSNP
rs1301535180	2030	dbSNP
rs1390847701	2034	dbSNP
rs924386801	2035	dbSNP
rs1230633543	2036	dbSNP
rs1366053509	2040	dbSNP
rs571352584	2041	dbSNP
rs192336099	2042	dbSNP
rs151044465	2043	dbSNP
rs1394262766	2044	dbSNP
rs1294844315	2051	dbSNP
rs566119649	2052	dbSNP
rs1044687293	2055	dbSNP
rs928852700	2056	dbSNP
rs1388975380	2058	dbSNP
rs1186175621	2061	dbSNP
rs536768948	2065	dbSNP
rs1286065226	2067	dbSNP
rs1047923422	2070	dbSNP
rs183705110	2075	dbSNP
rs570096203	2076	dbSNP
rs1278405213	2080	dbSNP
rs1038163276	2081	dbSNP
rs1343191103	2084	dbSNP
rs1006943824	2087	dbSNP
rs1273984244	2087	dbSNP
rs781487804	2088	dbSNP
rs996117258	2089	dbSNP
rs1309661939	2090	dbSNP
rs1410028417	2093	dbSNP
rs553317802	2093	dbSNP
rs780910472	2093	dbSNP
rs1459000894	2097	dbSNP
rs1271833485	2106	dbSNP
rs1166142372	2107	dbSNP
rs537715490	2117	dbSNP
rs1255811145	2120	dbSNP
rs955281274	2154	dbSNP
rs1184848393	2159	dbSNP
rs1483498205	2171	dbSNP
rs1008052662	2176	dbSNP
rs186174333	2178	dbSNP
rs1258590298	2179	dbSNP
rs1482938289	2182	dbSNP
rs1180561558	2184	dbSNP
rs577355330	2190	dbSNP
rs1410423654	2191	dbSNP
rs1419950262	2198	dbSNP
rs1265918218	2203	dbSNP
rs1243937044	2207	dbSNP
rs983967489	2208	dbSNP
rs1289965417	2226	dbSNP
rs1228847145	2230	dbSNP
rs916382396	2236	dbSNP
rs1326464591	2238	dbSNP
rs956031449	2241	dbSNP
rs1390872743	2249	dbSNP
rs989928753	2254	dbSNP
rs1461359000	2256	dbSNP
rs1416414083	2266	dbSNP
rs1161822571	2270	dbSNP
rs1473130025	2277	dbSNP
rs140370035	2278	dbSNP
rs969734565	2291	dbSNP
rs1453576789	2296	dbSNP
rs935040111	2302	dbSNP
rs1213208222	2303	dbSNP
rs1467079607	2304	dbSNP
rs1269944195	2309	dbSNP
rs1228721713	2313	dbSNP
rs1328250651	2319	dbSNP
rs979751828	2321	dbSNP
rs928911490	2326	dbSNP
rs938918742	2336	dbSNP
rs149960879	2337	dbSNP
rs908049886	2341	dbSNP
rs1306001705	2343	dbSNP
rs1375024059	2346	dbSNP
rs1224021489	2350	dbSNP
rs1392838541	2354	dbSNP
rs572079165	2355	dbSNP
rs1458055857	2358	dbSNP
rs1384655863	2363	dbSNP
rs1037815362	2374	dbSNP
rs1157237726	2375	dbSNP
rs1479121325	2377	dbSNP
rs1193012232	2383	dbSNP
rs1452671066	2387	dbSNP
rs1249763527	2389	dbSNP
rs900573859	2393	dbSNP
rs1446399692	2394	dbSNP
rs1281859039	2395	dbSNP
rs1309950784	2396	dbSNP
rs759833363	2402	dbSNP
rs1237062968	2410	dbSNP
rs932015067	2414	dbSNP
rs1366773772	2416	dbSNP
rs1483048846	2419	dbSNP
rs1297739574	2421	dbSNP
rs1203427926	2422	dbSNP
rs1235001758	2423	dbSNP
rs1481060285	2426	dbSNP
rs1190840205	2427	dbSNP
rs1265273232	2428	dbSNP
rs1455638896	2429	dbSNP
rs1174402908	2431	dbSNP
rs889923932	2434	dbSNP
rs778942508	2436	dbSNP
rs1403106847	2438	dbSNP
rs1173274154	2441	dbSNP
rs1395584301	2442	dbSNP
rs1007469231	2444	dbSNP
rs1189351210	2449	dbSNP
rs542348859	2452	dbSNP
rs1051710857	2456	dbSNP
rs560525735	2462	dbSNP
rs1019731505	2463	dbSNP
rs745846307	2467	dbSNP
rs890415360	2484	dbSNP
rs189970371	2487	dbSNP
rs10201459	2488	dbSNP
rs1168005798	2491	dbSNP
rs10193332	2493	dbSNP
rs1356082208	2495	dbSNP
rs1031976634	2496	dbSNP
rs111324357	2498	dbSNP
rs1365134642	2502	dbSNP
rs1450571580	2507	dbSNP
rs1442453226	2518	dbSNP
rs1312697029	2525	dbSNP
rs370542476	2529	dbSNP
rs543305134	2531	dbSNP
rs149085761	2532	dbSNP
rs969793370	2534	dbSNP
rs1409461308	2536	dbSNP
rs1164960371	2537	dbSNP
rs1226884251	2537	dbSNP
rs1275498291	2538	dbSNP
rs146052501	2545	dbSNP
rs1256510733	2546	dbSNP
rs1185598020	2547	dbSNP
rs111777267	2550	dbSNP
rs1203134523	2550	dbSNP
rs1435589797	2553	dbSNP
rs1271456298	2554	dbSNP
rs983998122	2558	dbSNP
rs1221378995	2562	dbSNP
rs1293048144	2563	dbSNP
rs1336174339	2563	dbSNP
rs796664791	2564	dbSNP
rs1263888718	2571	dbSNP
rs1352491101	2584	dbSNP
rs1035364260	2586	dbSNP
rs1308884455	2593	dbSNP
rs959666363	2594	dbSNP
rs1352803883	2595	dbSNP
rs983739723	2601	dbSNP
rs908103551	2605	dbSNP
rs1194300761	2606	dbSNP
rs982337996	2607	dbSNP
rs942243326	2608	dbSNP
rs761376747	2610	dbSNP
rs566457166	2621	dbSNP
rs1176298123	2629	dbSNP
rs922061908	2631	dbSNP
rs565755162	2632	dbSNP
rs1421306683	2633	dbSNP
rs553925473	2634	dbSNP
rs1163884128	2636	dbSNP
rs890470531	2637	dbSNP
rs935312169	2638	dbSNP
rs1053067394	2639	dbSNP
rs1325951196	2642	dbSNP
rs891694480	2644	dbSNP
rs1043331592	2646	dbSNP
rs1441738104	2647	dbSNP
rs1429152932	2668	dbSNP
rs577057592	2669	dbSNP
rs1389063799	2670	dbSNP
rs1272424092	2679	dbSNP
rs890028563	2680	dbSNP
rs1416926365	2683	dbSNP
rs750318640	2688	dbSNP
rs905660129	2689	dbSNP
rs1001297199	2694	dbSNP
rs756146430	2700	dbSNP
rs779862893	2701	dbSNP
rs530199782	2703	dbSNP
rs1466674698	2704	dbSNP
rs942913052	2708	dbSNP
rs1215600486	2711	dbSNP
rs1015207758	2717	dbSNP
rs1315279991	2724	dbSNP
rs548725152	2725	dbSNP
rs1235050629	2732	dbSNP
rs570061598	2732	dbSNP
rs963965580	2733	dbSNP
rs973644443	2734	dbSNP
rs922113186	2736	dbSNP
rs1463606458	2739	dbSNP
rs374049134	2741	dbSNP
rs1288069276	2742	dbSNP
rs537480587	2744	dbSNP
rs1451365629	2745	dbSNP
rs987535881	2746	dbSNP
rs1173906389	2747	dbSNP
rs139977608	2753	dbSNP
rs994219970	2757	dbSNP
rs779607791	2763	dbSNP
rs1169998327	2764	dbSNP
rs1451870427	2765	dbSNP
rs779063327	2769	dbSNP
rs748405712	2770	dbSNP
rs1239389848	2775	dbSNP
rs1211825984	2777	dbSNP
rs915206331	2780	dbSNP
rs888487170	2785	dbSNP
rs1278269013	2786	dbSNP
rs772117216	2787	dbSNP
rs1307939602	2788	dbSNP
rs372002656	2790	dbSNP
rs571077635	2791	dbSNP
rs905712479	2792	dbSNP
rs1313306534	2796	dbSNP
rs1413770665	2807	dbSNP
rs1373307790	2810	dbSNP
rs1169861689	2812	dbSNP
rs1462059687	2818	dbSNP
rs1001349389	2823	dbSNP
rs1023579490	2824	dbSNP
rs1427299613	2838	dbSNP
rs1416379619	2839	dbSNP
rs969690091	2842	dbSNP
rs535029651	2845	dbSNP
rs1207311810	2847	dbSNP
rs1346271194	2848	dbSNP
rs1250654996	2852	dbSNP
rs1447982326	2856	dbSNP
rs1323484832	2861	dbSNP
rs895558095	2868	dbSNP
rs1232458569	2869	dbSNP
rs1353113926	2870	dbSNP
rs1309496613	2873	dbSNP
rs1044277	2885	dbSNP
rs574720941	2886	dbSNP
rs771401142	2889	dbSNP
rs995512563	2890	dbSNP
rs1475093452	2891	dbSNP
rs1029178868	2897	dbSNP
rs1419942866	2897	dbSNP
rs914991523	2899	dbSNP
rs953571648	2900	dbSNP
rs533590609	2917	dbSNP
rs1489382773	2919	dbSNP
rs946421045	2928	dbSNP
rs746839070	2930	dbSNP
rs72781667	2931	dbSNP
rs1332455115	2934	dbSNP
rs1290026101	2941	dbSNP
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rs911502712	2945	dbSNP
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rs1388016014	2960	dbSNP
rs1041230595	2961	dbSNP
rs1327192639	2964	dbSNP
rs1461218066	2965	dbSNP
rs1392705023	2966	dbSNP
rs957002909	2974	dbSNP
rs1160707462	2975	dbSNP
rs1454494679	2982	dbSNP
rs1447475462	2988	dbSNP
rs575743051	2996	dbSNP
rs1179675650	2997	dbSNP
rs1255069553	3005	dbSNP
rs915240876	3009	dbSNP
rs1047212114	3017	dbSNP
rs1410737633	3020	dbSNP
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rs1467120815	3025	dbSNP
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rs1043017543	3039	dbSNP
rs1005578085	3040	dbSNP
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rs1024032091	3043	dbSNP
rs927179914	3053	dbSNP
rs1003834389	3054	dbSNP
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rs1034866005	3060	dbSNP
rs564751941	3061	dbSNP
rs937190042	3062	dbSNP
rs1383136512	3065	dbSNP
rs1311594297	3074	dbSNP
rs1377868688	3077	dbSNP
rs114968454	3086	dbSNP
rs774125391	3088	dbSNP
rs1395740374	3098	dbSNP
rs1173157073	3099	dbSNP
rs1334176099	3103	dbSNP
rs967753883	3106	dbSNP
rs1280166005	3121	dbSNP
rs1344421261	3142	dbSNP
rs541003522	3152	dbSNP
rs1278081998	3157	dbSNP
rs541913617	3158	dbSNP
rs11553491	3165	dbSNP
rs1212543309	3178	dbSNP
rs898846537	3211	dbSNP
rs994496302	3222	dbSNP
rs760886389	3228	dbSNP
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rs548691144	3242	dbSNP
rs1435665157	3245	dbSNP
rs773679364	3257	dbSNP
rs889358964	3268	dbSNP
rs1316740358	3275	dbSNP
rs1232885639	3284	dbSNP
rs1009058866	3287	dbSNP
rs527413256	3288	dbSNP
rs1432957243	3302	dbSNP
rs1019078377	3306	dbSNP
rs956865546	3307	dbSNP
rs1168457296	3314	dbSNP
rs1450713636	3315	dbSNP
rs1475068278	3315	dbSNP
rs1047241426	3328	dbSNP
rs563729620	3334	dbSNP
rs1168314401	3337	dbSNP
rs1394816262	3353	dbSNP
rs1208032849	3380	dbSNP
rs1439072927	3385	dbSNP
rs547363343	3386	dbSNP
rs766269346	3394	dbSNP
rs1339371508	3397	dbSNP
rs1329799844	3399	dbSNP
rs1022359056	3401	dbSNP
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rs1329682104	3428	dbSNP
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rs1394336407	3465	dbSNP
rs1166747294	3467	dbSNP
rs1475423581	3484	dbSNP
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rs980758297	3487	dbSNP
rs1470984816	3491	dbSNP
rs927232093	3501	dbSNP
rs1203288259	3508	dbSNP
rs552514294	3514	dbSNP
rs187324810	3527	dbSNP
rs1256733642	3528	dbSNP
rs1215891667	3534	dbSNP
rs1335955204	3534	dbSNP
rs749884833	3535	dbSNP
rs200373466	3537	dbSNP
rs1226802577	3544	dbSNP
rs1375876894	3562	dbSNP
rs1280209019	3569	dbSNP
rs917085267	3577	dbSNP
rs760119738	3585	dbSNP
rs1036546706	3590	dbSNP
rs1197404445	3593	dbSNP
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rs1461929402	3602	dbSNP
rs898902748	3603	dbSNP
rs1254371240	3607	dbSNP
rs1455051247	3610	dbSNP
rs190241197	3621	dbSNP
rs1371636040	3625	dbSNP
rs967784852	3630	dbSNP
rs1468177068	3631	dbSNP
rs1168902184	3641	dbSNP
rs1236843965	3643	dbSNP
rs1050048960	3669	dbSNP
rs766287571	3677	dbSNP
rs1007688113	3682	dbSNP
rs1469345758	3686	dbSNP
rs888743534	3693	dbSNP
rs547025074	3694	dbSNP
rs1009117391	3702	dbSNP
rs1318892955	3703	dbSNP
rs1285240650	3709	dbSNP
rs1223250286	3714	dbSNP
rs1019169875	3715	dbSNP
rs892650415	3716	dbSNP
rs1294764303	3719	dbSNP
rs1324674048	3728	dbSNP
rs1291505527	3731	dbSNP
rs1432654243	3735	dbSNP
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rs1345366375	3752	dbSNP
rs1229313679	3767	dbSNP
rs1157958149	3774	dbSNP
rs1009723765	3779	dbSNP
rs1398636668	3786	dbSNP
rs1270592341	3787	dbSNP
rs922871462	3791	dbSNP
rs1455083753	3792	dbSNP
rs1252929769	3797	dbSNP
rs200964662	3808	dbSNP
rs1189787213	3810	dbSNP
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rs1243092136	3818	dbSNP
rs1022834561	3824	dbSNP
rs982960657	3830	dbSNP
rs568308014	3835	dbSNP
rs1274447472	3836	dbSNP
rs1468545132	3840	dbSNP
rs1299133426	3845	dbSNP
rs1204112092	3846	dbSNP
rs1260228588	3850	dbSNP
rs1430848814	3853	dbSNP
rs201258181	3855	dbSNP
rs755779802	3855	dbSNP
rs763424953	3855	dbSNP
rs1165696132	3856	dbSNP
rs1491571475	3856	dbSNP
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rs1174532566	3857	dbSNP
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rs1211625161	3857	dbSNP
rs1259889993	3857	dbSNP
rs1420650252	3857	dbSNP
rs1430856361	3857	dbSNP
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rs199935532	3857	dbSNP
rs200765119	3857	dbSNP
rs202233084	3857	dbSNP
rs58077988	3857	dbSNP
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rs879070218	3857	dbSNP
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rs1299438357	3858	dbSNP
rs1355628234	3858	dbSNP
rs1393427223	3858	dbSNP
rs1397264511	3858	dbSNP
rs1399400809	3858	dbSNP
rs1413827724	3858	dbSNP
rs1463973035	3858	dbSNP
rs1491224707	3858	dbSNP
rs3210974	3858	dbSNP
rs557412114	3858	dbSNP
rs869213946	3858	dbSNP
rs1194291387	3860	dbSNP
rs1368271686	3861	dbSNP
rs1474315692	3873	dbSNP
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rs1395576306	3875	dbSNP
rs1420240771	3875	dbSNP
rs1188884957	3877	dbSNP
rs1475031811	3878	dbSNP
rs1176296817	3879	dbSNP
rs1287241373	3880	dbSNP
rs1382657760	3881	dbSNP
rs1383883824	3882	dbSNP
rs1318671100	3883	dbSNP
rs1480881282	3884	dbSNP
rs1354599020	3885	dbSNP
rs1231008977	3886	dbSNP
rs1294744574	3887	dbSNP
rs1335144845	3889	dbSNP
rs910015496	3897	dbSNP
rs1258465894	3899	dbSNP
rs1487106122	3906	dbSNP
rs1273631106	3917	dbSNP
rs1232284845	3923	dbSNP
rs55648041	3934	dbSNP
rs1206250416	3935	dbSNP
rs1338402146	3943	dbSNP
rs1257171864	3944	dbSNP
rs1391475503	3951	dbSNP
rs1484892772	3959	dbSNP
rs941455459	3963	dbSNP
rs1190585681	3967	dbSNP
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rs1045598107	3985	dbSNP
rs1418817341	4008	dbSNP
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rs1457592017	4018	dbSNP
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rs1366943079	4020	dbSNP
rs1156963813	4021	dbSNP
rs1184012366	4022	dbSNP
rs1365628151	4023	dbSNP
rs1237456872	4025	dbSNP
rs1176673196	4028	dbSNP
rs1469809673	4036	dbSNP
rs1253387624	4038	dbSNP
rs1455234463	4039	dbSNP
rs1212840156	4040	dbSNP
rs35694258	4058	dbSNP
rs926723134	4063	dbSNP
rs1262145073	4074	dbSNP
rs1239088656	4087	dbSNP
rs1315778789	4091	dbSNP
rs939378256	4097	dbSNP
rs557138097	4098	dbSNP
rs1373917018	4110	dbSNP
rs1326989730	4125	dbSNP
rs183705607	4136	dbSNP
rs1374848928	4144	dbSNP
rs754732387	4145	dbSNP
rs1412691884	4162	dbSNP
rs201434904	4164	dbSNP
rs117245337	4171	dbSNP
rs536766369	4175	dbSNP
rs1043548789	4177	dbSNP
rs903645257	4186	dbSNP
rs1379712768	4188	dbSNP
rs1007385428	4190	dbSNP
rs1455532235	4193	dbSNP
rs532798964	4195	dbSNP
rs1395679665	4197	dbSNP
rs1197880981	4201	dbSNP
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rs1263622332	4218	dbSNP
rs759948791	4223	dbSNP
rs1205304795	4225	dbSNP
rs1485348110	4228	dbSNP
rs1283176619	4229	dbSNP
rs1235940904	4232	dbSNP
rs1350661772	4236	dbSNP
rs965805122	4240	dbSNP
rs1239222308	4241	dbSNP
rs1329667792	4247	dbSNP
rs1320713554	4249	dbSNP
rs116442880	4250	dbSNP
rs188227371	4262	dbSNP
rs115489780	4265	dbSNP
rs146924959	4268	dbSNP
rs1395580973	4275	dbSNP
rs1480402503	4282	dbSNP
rs1477012963	4298	dbSNP
rs1374524088	4319	dbSNP
rs1175716086	4328	dbSNP
rs910135180	4330	dbSNP
rs569079725	4342	dbSNP
rs1173160409	4344	dbSNP
rs1394385077	4363	dbSNP
rs1432815899	4365	dbSNP
rs145053242	4370	dbSNP
rs10666550	4371	dbSNP
rs67155303	4372	dbSNP
rs193272661	4389	dbSNP
rs1277334819	4403	dbSNP
rs980952155	4423	dbSNP
rs563521929	4426	dbSNP
rs1343503860	4439	dbSNP
rs1272287805	4441	dbSNP
rs1228690063	4443	dbSNP
rs1340099186	4453	dbSNP
rs926725433	4459	dbSNP
rs1375148914	4463	dbSNP
rs56081686	4464	dbSNP
rs1376095212	4474	dbSNP
rs939429176	4478	dbSNP
rs992134546	4490	dbSNP
rs913870594	4491	dbSNP
rs869264027	4494	dbSNP
rs185663637	4504	dbSNP
rs1464949123	4509	dbSNP
rs563493947	4517	dbSNP
rs1369376830	4518	dbSNP
rs1043658435	4522	dbSNP
rs903755861	4523	dbSNP
rs1237177253	4531	dbSNP
rs943219452	4539	dbSNP
rs1275782646	4544	dbSNP
rs1307291693	4559	dbSNP
rs1202951032	4561	dbSNP
rs1038841318	4566	dbSNP
rs530991455	4572	dbSNP
rs1481111934	4580	dbSNP
rs546015070	4585	dbSNP
rs1193039930	4594	dbSNP
rs1329503420	4596	dbSNP
rs1251239159	4604	dbSNP
rs1465065791	4612	dbSNP
rs188991745	4616	dbSNP
rs1195425976	4617	dbSNP
rs997231375	4620	dbSNP
rs113362373	4621	dbSNP
rs886143514	4622	dbSNP
rs1427688115	4623	dbSNP
rs1232987907	4635	dbSNP
rs1005885250	4638	dbSNP
rs1355888122	4644	dbSNP
rs1017636401	4645	dbSNP
rs546983602	4647	dbSNP
rs962976092	4652	dbSNP
rs1216016317	4653	dbSNP
rs568368881	4654	dbSNP
rs529567133	4656	dbSNP
rs1391668844	4658	dbSNP
rs1443668910	4660	dbSNP
rs550730478	4661	dbSNP
rs1361943269	4663	dbSNP
rs1213157657	4664	dbSNP
rs1298244076	4674	dbSNP
rs569145212	4674	dbSNP
rs1310104453	4680	dbSNP
rs1445876702	4688	dbSNP
rs1308247067	4696	dbSNP
rs1374666143	4702	dbSNP
rs1213314336	4705	dbSNP
rs1327658630	4706	dbSNP
rs1441435173	4707	dbSNP
rs1271274475	4709	dbSNP
rs1348909836	4709	dbSNP
rs1033824534	4713	dbSNP
rs4665651	4714	dbSNP
rs1247192163	4732	dbSNP
rs992164269	4736	dbSNP
rs111507593	4737	dbSNP
rs570415857	4742	dbSNP
rs796889579	4742	dbSNP
rs1489033472	4743	dbSNP
rs7422667	4744	dbSNP
rs1448965544	4745	dbSNP
rs1286740056	4750	dbSNP
rs1477910770	4754	dbSNP
rs1163767405	4767	dbSNP
rs570762264	4775	dbSNP
rs539694064	4782	dbSNP
rs377336770	4783	dbSNP
rs925208792	4786	dbSNP
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rs943269803	4787	dbSNP
rs1039285725	4788	dbSNP
rs1297026431	4792	dbSNP
rs1417376986	4796	dbSNP
rs769815746	4796	dbSNP
rs901634827	4796	dbSNP
rs1290937608	4812	dbSNP
rs1047548073	4814	dbSNP
rs886179432	4818	dbSNP
rs1341525059	4825	dbSNP
rs1005914864	4833	dbSNP
rs1015909350	4834	dbSNP
rs1291653587	4835	dbSNP
rs574755853	4847	dbSNP
rs1487328237	4848	dbSNP
rs1282592762	4849	dbSNP
rs1002427348	4855	dbSNP
rs1311538311	4855	dbSNP
rs1233942698	4868	dbSNP
rs1034266491	4874	dbSNP
rs1216169616	4874	dbSNP
rs1397783502	4874	dbSNP
rs746744218	4874	dbSNP
rs1356758357	4875	dbSNP
rs960900600	4879	dbSNP
rs992272691	4884	dbSNP
rs1359158532	4890	dbSNP
rs147289883	4893	dbSNP
rs202028560	4898	dbSNP
rs1243566951	4899	dbSNP
rs191436295	4900	dbSNP
rs557177494	4904	dbSNP
rs1187034994	4906	dbSNP
rs1476972953	4921	dbSNP
rs1259626390	4928	dbSNP
rs1182589697	4934	dbSNP
rs1254936169	4935	dbSNP
rs1482879183	4943	dbSNP
rs183610040	4944	dbSNP
rs1450176525	4945	dbSNP
rs1254226755	4961	dbSNP
rs1206319957	4965	dbSNP
rs966741116	4967	dbSNP
rs55683506	4968	dbSNP
rs576442635	4978	dbSNP
rs1216346232	4983	dbSNP
rs925272099	4988	dbSNP
rs1312798031	4993	dbSNP
rs1394998531	4994	dbSNP
rs964988334	5006	dbSNP
rs1301565824	5014	dbSNP
rs974725002	5015	dbSNP
rs968155819	5018	dbSNP
rs1170419869	5027	dbSNP
rs1361800152	5027	dbSNP
rs1370479869	5031	dbSNP
rs980810675	5035	dbSNP
rs1254204441	5036	dbSNP
rs933170951	5040	dbSNP

- Cell, 2010

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.