miRTarBase - #MIRT471524


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pre-miRNA Information
pre-miRNA hsa-mir-664a   
Genomic Coordinates chr1: 220200538 - 220200619
Description Homo sapiens miR-664 stem-loop
Comment This miRNA sequence overlaps an annotated snoRNA, ACA38b. However, both miR and miR* sequences are identified in reference , and the sequence is homologous with rat mir-664.
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-664a-3p
Sequence 49| UAUUCAUUUAUCCCCAGCCUACA |71
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN30457627 12 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1478242335 2 dbSNP
rs1042905485 5 dbSNP
rs908858734 6 dbSNP
rs1229753248 8 dbSNP
rs770101636 12 dbSNP
rs746047168 14 dbSNP
rs1170225715 15 dbSNP
rs1404740911 16 dbSNP
rs1393962832 17 dbSNP
rs1377901643 18 dbSNP
rs1313271494 19 dbSNP
rs1416447585 20 dbSNP
rs1368463251 21 dbSNP
rs1167925254 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
miRNAs in Extracellular Vesicles
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol PCGF3   
Synonyms DONG1, RNF3, RNF3A
Description polycomb group ring finger 3
Transcript NM_006315   
Expression
Putative miRNA Targets on PCGF3
3'UTR of PCGF3
(miRNA target sites are highlighted)		 
>PCGF3|NM_006315|3'UTR
   1 ATGGTGCCACACAGCGCCCACAGACTGGGCCCTCGCACCCTTGGGTGCTCCCGGCCGCCGCGCTTAAGAACATTGCCTCT
  81 GGGTGTCATGTGGACCAGACTTCTGAATAGAGAATATTTATAACTTTTGTATGAGAGAGAATTCACACTCAACAAGACAC
 161 TACCAGCACCACGTTTACAGAGGATGAAAACACTTCACAGTCTCCCAGAGCCGATCGTCCTCTCCCCCGCCCCACCCCGT
 241 GCTTCAGCCTTGCAGGGAGAGTGATGCTCCAGGCAACACGGTTCTGAGTCACCTTCTGACACGAGCTCCCTCTGCTTGCT
 321 TTCCAGGTCTTGAAAATCTGAATTCACTTCAGTTTAGTTTATGAATTTTAGGTTTCATGATAAGCCTCAAGTGTAGTTGG
 401 ACTTTTATTGAATCCTTCCTAAGTTATTGAAAAAATGTCTTTTCATGGTGAATGACAATATTTATGTTGCCTTTAGCTTC
 481 TTGAAGATTTAGAAGTTATATAAAAAATTAATTTAAAAGCAAACCAAAAGAGGTTTCCATTAACATTATGATTTAACCAT
 561 TGTATTTAATTTCCCACCTTATGAAACACAACAGCAGCTCCCTGACTGGTTCGCCTTTCATTGTGTGAGGTCGGCACTTG
 641 GACTCACTCAGAACTGTCGCTCACCTGTGGCTGACACACCCAGCCCTGGAAACGGGGCCCCAGACGCCACGTCGGGATTT
 721 CTGACATGCTCAGCAGGTAGACCAGAGGCCGTGTGACCAGCTCAGTGCTGGTTTACGGAACAACTCTTACTTTTAAAAAT
 801 TACTTGTTCCCCCAAATTGTTGAGTGCCGCCGTTTGGTTTCCTATGTTTTCTTTCCCTGTTTTGATTTTGCTGAAGGGAG
 881 AGGTGGTGGTGGTTAGGATCAGAGCTCTCCTGGCATCCGTGGGGAGGATTTGCTGGTGGTGGCTTCGGGCTCATGCCCAG
 961 ACACACTCACTGCCCCGTCTGTCCAAGGCCTCCCCTTCCCCTTTGCTGGTGGGAGGAGCTCGTGTGCTCCTTGGCCGCTT
1041 ACTGGAAGGGCGTTTTTCAGAGCTGCAGGGACAGGGTGAGCAGCTGAAGGGCTAGGAGGGAAGCCGGCCCCCGCTCTGCA
1121 GAAGCTGCATTTCAGCTGAATCTGTGTTTCAGCCTCAGTTGGTTGCACCGTTAGCCCCTCTCCTCCCGGATGGTCATGTT
1201 TTTGTCACATTAGAGAATAAACAGCCACACACACATTTTTTTTTTTCCTTTAAAACAGTAACTTGGAAATATGAAAAGGC
1281 CAGAAGGAGGAGCAAGGGCTGTTTTCTGGAGTGGTTGAGGTGTTGTCCTGCAGTTGTCATTGTCTTCTCCACCGGGCTGT
1361 TCCCATTTATTTCCTGTGGAACTGAATCCCTCCTCCCTCCACTCCTTGGGAGCCCAGGTGGTCCTTGGCCACCATTCAGG
1441 CTTTCCAAGAAGCCAACCACCTTGGAGATTTTTTTTCTTGAATTTCGCTGTTTTCTTCTGCTTCCTTTAGATAAAAAGCA
1521 GCTCAAGAGACCTTATCTTAGGGATGAGAAAAACATGCATATTAATTCCATCTGAGTGATTGTCAGTGTAAGGCCTTTTA
1601 AAACAAAAGCAAGTTCTTTGTTAGGAATTGGTCAAAATTCATCTCTTTCTTTAAGCCCATCAACTCCCAGGACGGTTTGA
1681 GTTACTCAGTTACCTAAGCTTGCTATTCATCCAAATCATTTTCTAGAGTCACTGTATAAGGGTCTATGAGTAGCTGTGTA
1761 TGAATAAATATTACCTGTCTACCTCAAAATACACATACTGCTGAAGCATTCTGTACAACCGTGTGTTATCACAGTGCAGT
1841 TTTAAGTGTAACGTTAGAACTTAGGCATTTTCCTGTGTGGCGGAATAAGAAAGGATTAAACAGTTACAAGCCTCCAAATT
1921 CAAATAAAATTAAATCACAGTTCAGATGAAACTGAATATCATTGTAATAATCTCATAATATATATTTGTAACTTTGTAGC
2001 TATCTTTGAAATCACTTGACTTTGCAATGGTGCTAAGCTGATAGATTTAAATACACAGACGGGCGAGTGGCGCCCGTGTC
2081 GATGTCTTCAGCCAGTGGTGACCCTGCTTTTGTAACCGCGTTAACCTGACAAAACCTCAGCAGCAGAAGTCCCTATTTTT
2161 CTAGGAGTTCATCGTGCAGACAGTCTTCACTACAGGACTCGGCCCTGGGGCCTCTGCCTCTCGTCTGACCTTGCAGCCTT
2241 AGTCGTTGGAGGCTGGAGCGCAATGGCCCTGCCGTCTGTGGAGCCTCTGGGCGGCCTTCTTTCCTTTCTGTCAACCTCTC
2321 ATTTCACAGAAAAAGGCTGAATTTCATTTTTTCCAGCATGAAAGCCAGGATCGGTTAGTGGTTGGATTCTATTGGTTTTT
2401 TTTTTTTAAACAGATGGAGTTACTGTGAAGAAGTTTTCACAACTATTTATGCTGGTAAAACAAATGCTGTTAAATCACCT
2481 TATGCGTCGTTTTCAACAGCAGTGGGGCTAATTACCCGGAATACGGTCTCACCGATGCAGTTTTCATGGACATAGAAAAT
2561 TCAAATAGAATATATAATATTGAATTTAAGATTTGGGGGGTTAAAAAAGAAAACTTAACTTTATAAAATTATTTATTCTA
2641 TTTTAAGCCTTCTATCATATTTTCCCATCCAATTGTTTGGTTTCAGTGGTCCAGCTTTATTTACAGGCATATAAAATGAA
2721 ATTGTGAGATGTTTTGCAAGCTTCTTTTTACTTTGAGTAGCTTTTAATTTGTATGTTTTTATGTGGATGAAGAGCATTTT
2801 TTATGCTTTTGTGCAATAGGTTCCAATATGCATTTATTAGACATCTGTTTAAATGGTAATGTAGCATTTATTTTGCTAAA
2881 TTGAAAGGGAACATAGATGGAATTCCAAAATATGTACATTCAGCTGTTTGGTTTTTCGTTTTTCATTGTTATTATTGTGA
2961 GAATGCTGTTATTGGGGTTGTGTGTGAGTGCCCGTCAGCCAGTGATGCCTCGGGCCACGCTGTGGGGCCACCTCAGTCCT
3041 GCCTGGGTCCTGGTGCCTTGGACCCCACGTGCTTGTGGCCAGGCTGCCCCTGGGCAGGGCCATGTGGCCTCAGACCACAA
3121 GAGCGGAGCTGCCCTGGCCCAAGCACTGCAGCTGCCTGCACCCCCGGGCTTCGCAGCCTTGCTTGTTTTCTCTGAACAGC
3201 AACAGAACAGTGTTCACAGCGATTCAAAGGGTGGCATTGGGTTGGACGTTCTGGGTACAAGCCAACCTAGTCCCACGTTG
3281 TACGTGAATGTTTAATGTGCTCTCAAAACATGGAAAATAAGTTTAGTGCACATAGCTAAATCACAAAACATCCAATTTCT
3361 CTGTTTCCTCAGGAAGTCATTACTGCGCCACCACATCACATGACCTTAACATGATCAATGTATTTCTCTGCCTTGACATT
3441 TAAATACATAAATTGAGATAAGTAGATTAGAAAATCATTCAAATGATACCATAATTTGTACGGGACAGGGTGCGGGCAAT
3521 GGCCACGTGGCCAAGGCCCTGCAGGAACGCGCCGAGGTCTCCCTCACCCTCCAGGTGTCCTTCGCACCCAACAGTGCGTC
3601 TGAGGAACGAGCTGCAGTTTGAGCGTTCCCCTGAGATGTGCGTAGCCTCCGTGTAAATGTCCACTCCCATGGCTTAATTG
3681 CCTATCAGACGCATTTTCCCAGACGAAAGCAATGTTGGGTTGGGGAAGACAGTGCAGCCACCCAGCCTTTACCAGCAGCG
3761 TACGGCAGACGAAGGCAGTCGAGGTGTGGAGGTGATCACGAAGATACATGTGTTTGACTGTTTAATTTGAAAGTTTACAT
3841 TTTTTATGCTTTGTGTTGGTGTGTAATTTTTGTACTCTTGGTGGCTAGTTTTTGTCAAATCTTTTTTGGAATATTGCTTA
3921 AATGTTTTGATTTTATGATAGTGAAGCTTGTATTCAGTGTTTTGCCAATTAATATTATATGCTTGTAATAAAAGCAAAAG
4001 AAAAGCTTAAGTGAAAGTGTTTCTGGCTGGAAATGTATTACATAAATCATTTGTATGAGCATGAGAGATGACTTGCTCAT
4081 GGGATGAGCAATGCTGTGGGTATTGGATGGACCACTCAGGCAGCCTGGCCGCACACACACACATGCATGCTACATATGTG
4161 TACGCTCAGACCACATGCCTGCACATATGTCCACACACCAGCCCACGGCTCCCTTCCTCACCCCAGCCCTCCCCACTCCC
4241 AGGTTAACCAATGTCTCGATTTGCTTCAGGCGGCATTTGTAAACTGTCACCCTGCTTGCAAACCCTCATTTAAATTGGTC
4321 CAGCATTTGCTACCAGAGTTTAGGCCACAAACTTTGTAAAGCTCAGTTTGTCTCCTTGCAGAAAGAGGTTGCTGCAGTTT
4401 GGAGCTGGTTATGCCAAGGAAAATACGGCTAAAAAAGAACTTACTGATTCCCATAGGTGTGTCAACTGACAAATGAATGT
4481 TCCATCTCCCTACGACAATTTGCTGCCCCTCCCCAAAAAAAGCACTATGGCCAAAATTTCAGTTTTTAAAGGTTAAGTAA
4561 AATACAACAATTCTGAAACTCTTAAGAGAACCAGAATTGGAAGGAAAGGAGAATGGCCAAAATTATATTCTCACAACCTA
4641 AAGCAGTAAACTTTAAAAATAGGTTCAGTCTTAGACTTGACTTAATTGACTTAGGCTGGGCATAGTGGCTCACACCTGTA
4721 ATTCCAGCACCGTAGGAGGCCAAGGCAGGCTGATCATCTGAAGTCGGGAGTTCGAGACCAGCCTGGCTAACATGGTGAAA
4801 TCCCGTCTCTACTAAAAAATATAAAAATTAGCCGGGTGTGGTGGCAGGGGCCTGTAGTCCCAGCTACTCAGGAGGCTGAA
4881 GCAGGCGAATCGCTGGAACAC
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1 
miRNA  3' acAUCCGACCC------CUAUUUACUUAu 5'
            |||| || |      || |||||||| 
Target 5' caTAGG-TGTGTCAACTGACAAATGAATg 3'
 4452 - 4479 158.00 -11.50
2 
miRNA  3' acAUCCGACCCCUAUUUACUUAu 5'
            || |||| | ||:||| ||| 
Target 5' agTA-GCTGTGTATGAATAAATa 3'
 1749 - 1770 140.00 -10.70
3 
miRNA  3' acaUCCG-ACCCCUA-UUUACUUau 5'
             |||| |    || |||||||  
Target 5' tacAGGCAT----ATAAAATGAAat 3'
 2702 - 2722 130.00 -6.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN28613582 6 COSMIC
COSN30149195 24 COSMIC
COSN30154830 31 COSMIC
COSN31504337 33 COSMIC
COSN31495130 35 COSMIC
COSN26575131 57 COSMIC
COSN31511869 59 COSMIC
COSN30193479 60 COSMIC
COSN30110786 61 COSMIC
COSN30134387 62 COSMIC
COSN14123787 63 COSMIC
COSN26439265 69 COSMIC
COSN30138542 71 COSMIC
COSN30564073 84 COSMIC
COSN30501361 95 COSMIC
COSN31501017 104 COSMIC
COSN30689920 116 COSMIC
COSN31780535 140 COSMIC
COSN31561839 199 COSMIC
COSN26596401 240 COSMIC
COSN9241407 303 COSMIC
COSN31516741 304 COSMIC
COSN29893456 345 COSMIC
COSN9241412 455 COSMIC
COSN2044618 466 COSMIC
COSN32104975 751 COSMIC
COSN32064581 807 COSMIC
COSN22874375 858 COSMIC
COSN32058712 991 COSMIC
COSN2044653 1159 COSMIC
COSN20099689 1247 COSMIC
COSN27384657 1247 COSMIC
COSN15152823 1285 COSMIC
COSN9241443 1481 COSMIC
COSN217054 1557 COSMIC
COSN26576362 1653 COSMIC
COSN31595287 1668 COSMIC
COSN10035081 1836 COSMIC
COSN28198141 1924 COSMIC
COSN28204808 2053 COSMIC
COSN22150478 2102 COSMIC
COSN24300660 2120 COSMIC
COSN17462619 2154 COSMIC
COSN31481310 2246 COSMIC
COSN31541634 2260 COSMIC
COSN31487901 2282 COSMIC
COSN6509476 2298 COSMIC
COSN20099690 2407 COSMIC
COSN27498638 2408 COSMIC
COSN7643774 2408 COSMIC
COSN32016966 2517 COSMIC
COSN9241496 2591 COSMIC
COSN26579858 2865 COSMIC
COSN29097079 2866 COSMIC
COSN25033266 2937 COSMIC
COSN26669321 2939 COSMIC
COSN31589493 3013 COSMIC
COSN31479691 3051 COSMIC
COSN2044719 3094 COSMIC
COSN17282734 3204 COSMIC
COSN30176806 3226 COSMIC
COSN20883093 3236 COSMIC
COSN22981918 3313 COSMIC
COSN5017419 3388 COSMIC
COSN31593434 3528 COSMIC
COSN6581806 3550 COSMIC
COSN31597025 3599 COSMIC
COSN31590835 3692 COSMIC
COSN6843622 3733 COSMIC
COSN21857995 3737 COSMIC
COSN31537473 3761 COSMIC
COSN28794565 3764 COSMIC
COSN15668384 3765 COSMIC
COSN26638050 3813 COSMIC
COSN21859526 4082 COSMIC
COSN21860044 4111 COSMIC
COSN6843634 4208 COSMIC
COSN16489252 4401 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs779063874 2 dbSNP
rs1291341212 3 dbSNP
rs953555111 4 dbSNP
rs750654963 5 dbSNP
rs73058482 6 dbSNP
rs200755246 7 dbSNP
rs746755148 9 dbSNP
rs1234178879 10 dbSNP
rs768479514 11 dbSNP
rs1182533539 12 dbSNP
rs781181865 14 dbSNP
rs187131626 16 dbSNP
rs74505207 17 dbSNP
rs573528597 18 dbSNP
rs753224837 19 dbSNP
rs918279604 19 dbSNP
rs770521054 20 dbSNP
rs1329610601 22 dbSNP
rs540561961 25 dbSNP
rs756651025 26 dbSNP
rs1445921850 27 dbSNP
rs1314581619 28 dbSNP
rs761034482 29 dbSNP
rs930990238 30 dbSNP
rs1247874098 31 dbSNP
rs201142690 35 dbSNP
rs777184152 36 dbSNP
rs761850506 37 dbSNP
rs1275039641 38 dbSNP
rs1440127983 39 dbSNP
rs1202518786 41 dbSNP
rs765332768 44 dbSNP
rs1446131906 45 dbSNP
rs758720643 47 dbSNP
rs1371763339 49 dbSNP
rs373752823 52 dbSNP
rs551951122 53 dbSNP
rs577279947 54 dbSNP
rs1432726338 56 dbSNP
rs191166241 57 dbSNP
rs562928926 58 dbSNP
rs149492411 60 dbSNP
rs921433291 61 dbSNP
rs374940813 62 dbSNP
rs548408451 63 dbSNP
rs1195003984 66 dbSNP
rs1051247087 68 dbSNP
rs1255977851 72 dbSNP
rs1458797036 73 dbSNP
rs914172888 73 dbSNP
rs1198927217 76 dbSNP
rs368273258 78 dbSNP
rs1010915535 80 dbSNP
rs1464429808 88 dbSNP
rs1408913911 93 dbSNP
rs1421563753 97 dbSNP
rs1173699615 101 dbSNP
rs538558817 105 dbSNP
rs945686778 106 dbSNP
rs1369547786 107 dbSNP
rs1041370124 111 dbSNP
rs1419882131 113 dbSNP
rs552407686 115 dbSNP
rs904210440 115 dbSNP
rs1264870597 121 dbSNP
rs1200971206 124 dbSNP
rs1029382243 125 dbSNP
rs999946961 125 dbSNP
rs1253732121 129 dbSNP
rs1240650780 130 dbSNP
rs953483949 132 dbSNP
rs1019436647 133 dbSNP
rs534510831 133 dbSNP
rs556128689 134 dbSNP
rs1414412397 136 dbSNP
rs527615629 138 dbSNP
rs918511080 140 dbSNP
rs1336350252 144 dbSNP
rs781283747 145 dbSNP
rs1400090383 149 dbSNP
rs931188741 150 dbSNP
rs983816603 151 dbSNP
rs143923954 152 dbSNP
rs748335745 153 dbSNP
rs1188069337 157 dbSNP
rs1254050252 160 dbSNP
rs1217984311 161 dbSNP
rs947808199 163 dbSNP
rs1276033288 167 dbSNP
rs763591062 167 dbSNP
rs570136134 171 dbSNP
rs906741029 173 dbSNP
rs1052998822 174 dbSNP
rs1320909203 177 dbSNP
rs1400637223 181 dbSNP
rs537417971 184 dbSNP
rs1296519433 185 dbSNP
rs1426775037 187 dbSNP
rs894073497 191 dbSNP
rs1163590740 193 dbSNP
rs1472374661 194 dbSNP
rs543449488 196 dbSNP
rs773268272 199 dbSNP
rs1004558502 200 dbSNP
rs866945121 201 dbSNP
rs1195802812 203 dbSNP
rs1016931397 206 dbSNP
rs1029020566 207 dbSNP
rs889104708 208 dbSNP
rs1446899502 211 dbSNP
rs963065575 213 dbSNP
rs975487231 214 dbSNP
rs1426172317 215 dbSNP
rs1018982874 217 dbSNP
rs763957999 218 dbSNP
rs1025869837 219 dbSNP
rs1388318812 220 dbSNP
rs1172658544 221 dbSNP
rs553753073 229 dbSNP
rs868639655 230 dbSNP
rs916276294 230 dbSNP
rs969041228 231 dbSNP
rs567770431 232 dbSNP
rs1303474162 233 dbSNP
rs1450163448 236 dbSNP
rs1384395973 237 dbSNP
rs914100942 239 dbSNP
rs567645677 240 dbSNP
rs1225380974 242 dbSNP
rs535174531 245 dbSNP
rs927705856 246 dbSNP
rs1368442000 253 dbSNP
rs1274420568 256 dbSNP
rs555186919 259 dbSNP
rs1219016543 262 dbSNP
rs181505560 263 dbSNP
rs925634512 269 dbSNP
rs935674889 271 dbSNP
rs1055511659 273 dbSNP
rs1415645313 275 dbSNP
rs1190212443 280 dbSNP
rs894249548 280 dbSNP
rs1014069472 281 dbSNP
rs1256675843 282 dbSNP
rs1212870305 285 dbSNP
rs1045580252 291 dbSNP
rs1051111203 292 dbSNP
rs1256036892 293 dbSNP
rs763503473 293 dbSNP
rs1004123302 294 dbSNP
rs1375756533 297 dbSNP
rs1017269857 302 dbSNP
rs866322095 303 dbSNP
rs997272086 304 dbSNP
rs1040316041 305 dbSNP
rs62294079 309 dbSNP
rs993965820 310 dbSNP
rs955443769 311 dbSNP
rs1025498193 316 dbSNP
rs1381726484 319 dbSNP
rs1158911538 324 dbSNP
rs1439404441 327 dbSNP
rs1236749329 329 dbSNP
rs1184023693 330 dbSNP
rs1483861133 343 dbSNP
rs986871040 344 dbSNP
rs1265763301 348 dbSNP
rs1005508036 351 dbSNP
rs914070134 351 dbSNP
rs1177092112 353 dbSNP
rs1286961033 354 dbSNP
rs1363250842 357 dbSNP
rs558951172 358 dbSNP
rs969259447 361 dbSNP
rs967316078 362 dbSNP
rs979675391 373 dbSNP
rs925531019 374 dbSNP
rs202104667 379 dbSNP
rs927592842 381 dbSNP
rs1298369796 387 dbSNP
rs1418705714 388 dbSNP
rs1167306994 389 dbSNP
rs1378168066 389 dbSNP
rs1156693435 391 dbSNP
rs7336 392 dbSNP
rs988284040 393 dbSNP
rs1489274060 394 dbSNP
rs991578321 395 dbSNP
rs578057826 396 dbSNP
rs879083234 398 dbSNP
rs80202333 399 dbSNP
rs1388104706 403 dbSNP
rs1322139420 405 dbSNP
rs949776986 406 dbSNP
rs1301565013 407 dbSNP
rs767851864 409 dbSNP
rs1237323760 413 dbSNP
rs1287609496 415 dbSNP
rs1355019594 419 dbSNP
rs1040370895 420 dbSNP
rs755510761 421 dbSNP
rs886905407 422 dbSNP
rs939849930 423 dbSNP
rs557954607 424 dbSNP
rs993624949 430 dbSNP
rs185884784 432 dbSNP
rs1489683818 435 dbSNP
rs887829848 435 dbSNP
rs898419888 437 dbSNP
rs1211663657 440 dbSNP
rs575026015 440 dbSNP
rs80327149 443 dbSNP
rs1438137198 444 dbSNP
rs1217430823 445 dbSNP
rs1180565196 449 dbSNP
rs1381045647 450 dbSNP
rs1420191495 452 dbSNP
rs1366536069 453 dbSNP
rs1164027013 455 dbSNP
rs1467558778 458 dbSNP
rs1170634347 459 dbSNP
rs1347847632 459 dbSNP
rs1464070101 460 dbSNP
rs1459254438 462 dbSNP
rs1293968127 463 dbSNP
rs1199749966 464 dbSNP
rs1265589828 465 dbSNP
rs1432818462 465 dbSNP
rs1028261419 466 dbSNP
rs1375674899 471 dbSNP
rs1458941691 477 dbSNP
rs776209094 477 dbSNP
rs1238667183 481 dbSNP
rs1197936039 483 dbSNP
rs560326538 487 dbSNP
rs1257230701 491 dbSNP
rs1310765258 493 dbSNP
rs1449413956 493 dbSNP
rs878958234 495 dbSNP
rs1378116105 497 dbSNP
rs1331199719 500 dbSNP
rs1021003256 502 dbSNP
rs1405070601 502 dbSNP
rs1034715568 503 dbSNP
rs754776470 508 dbSNP
rs966865667 510 dbSNP
rs987950027 513 dbSNP
rs980028376 515 dbSNP
rs1228202563 520 dbSNP
rs1441241849 524 dbSNP
rs527469306 524 dbSNP
rs1323809664 526 dbSNP
rs1222763964 529 dbSNP
rs959879217 531 dbSNP
rs572768928 538 dbSNP
rs967788501 538 dbSNP
rs1200483638 540 dbSNP
rs1257876532 545 dbSNP
rs1456587286 546 dbSNP
rs1277667353 547 dbSNP
rs915570214 548 dbSNP
rs1238817507 550 dbSNP
rs865969463 552 dbSNP
rs1241891183 553 dbSNP
rs949705490 556 dbSNP
rs1237388797 558 dbSNP
rs1308990374 558 dbSNP
rs1181146446 559 dbSNP
rs1342763421 560 dbSNP
rs1335471765 564 dbSNP
rs1395484490 565 dbSNP
rs375533727 569 dbSNP
rs554184910 569 dbSNP
rs1425549845 570 dbSNP
rs1165184306 574 dbSNP
rs981147916 576 dbSNP
rs908305337 578 dbSNP
rs939839675 583 dbSNP
rs1038597236 585 dbSNP
rs1370078469 586 dbSNP
rs898351817 586 dbSNP
rs1188170203 588 dbSNP
rs976290740 589 dbSNP
rs546097790 590 dbSNP
rs764885784 592 dbSNP
rs1284933626 594 dbSNP
rs779642561 599 dbSNP
rs1358941509 602 dbSNP
rs1446656893 602 dbSNP
rs1244713756 604 dbSNP
rs891093580 605 dbSNP
rs1280164485 610 dbSNP
rs1354175546 610 dbSNP
rs1008187036 613 dbSNP
rs116108910 614 dbSNP
rs1398669408 617 dbSNP
rs982950662 618 dbSNP
rs902612163 624 dbSNP
rs1229436119 626 dbSNP
rs1000988030 630 dbSNP
rs1032908215 633 dbSNP
rs1044945393 634 dbSNP
rs1195190565 639 dbSNP
rs1241115094 642 dbSNP
rs1477876714 642 dbSNP
rs1316472395 644 dbSNP
rs531211327 650 dbSNP
rs991033676 651 dbSNP
rs749920953 652 dbSNP
rs77658869 659 dbSNP
rs1442132639 660 dbSNP
rs1333290996 661 dbSNP
rs1260600219 662 dbSNP
rs540121351 673 dbSNP
rs1339944333 674 dbSNP
rs1268579974 678 dbSNP
rs971027243 680 dbSNP
rs1331967949 681 dbSNP
rs1323937316 684 dbSNP
rs567711044 686 dbSNP
rs1484174437 687 dbSNP
rs1392144088 689 dbSNP
rs1172766184 690 dbSNP
rs1188606379 694 dbSNP
rs1465626449 694 dbSNP
rs1422589447 695 dbSNP
rs1165706989 696 dbSNP
rs1009654091 698 dbSNP
rs1478803244 698 dbSNP
rs908229299 701 dbSNP
rs766249593 706 dbSNP
rs973888467 707 dbSNP
rs1199836519 711 dbSNP
rs529019847 712 dbSNP
rs561693973 714 dbSNP
rs1049594482 715 dbSNP
rs966173850 716 dbSNP
rs1345952751 717 dbSNP
rs1274512900 719 dbSNP
rs547147689 724 dbSNP
rs567068446 725 dbSNP
rs376575278 726 dbSNP
rs1331588243 727 dbSNP
rs1042770852 728 dbSNP
rs1167662632 738 dbSNP
rs985215964 743 dbSNP
rs1172659645 751 dbSNP
rs1425375735 751 dbSNP
rs534092481 751 dbSNP
rs1452900914 752 dbSNP
rs573292801 754 dbSNP
rs1382542282 756 dbSNP
rs1179730556 758 dbSNP
rs559205360 759 dbSNP
rs1001358357 764 dbSNP
rs1338821562 766 dbSNP
rs571206099 769 dbSNP
rs751455600 771 dbSNP
rs939171393 772 dbSNP
rs1240649811 777 dbSNP
rs538526952 778 dbSNP
rs1280773128 779 dbSNP
rs1296405426 779 dbSNP
rs895264111 781 dbSNP
rs1312868495 782 dbSNP
rs190889708 785 dbSNP
rs1009461575 786 dbSNP
rs1043805614 786 dbSNP
rs1418887673 787 dbSNP
rs544203853 787 dbSNP
rs1012438128 789 dbSNP
rs1007298264 790 dbSNP
rs1184119985 791 dbSNP
rs1256876948 792 dbSNP
rs1208904175 794 dbSNP
rs1487305093 800 dbSNP
rs753437217 808 dbSNP
rs1216179013 809 dbSNP
rs965734257 810 dbSNP
rs574861366 814 dbSNP
rs1229947779 816 dbSNP
rs1195556685 823 dbSNP
rs562394486 825 dbSNP
rs542333050 829 dbSNP
rs115135810 830 dbSNP
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rs1343813449 834 dbSNP
rs1359176114 838 dbSNP
rs572217460 841 dbSNP
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rs543433112 843 dbSNP
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rs1485049240 847 dbSNP
rs1258735805 851 dbSNP
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rs114620436 856 dbSNP
rs1368308758 857 dbSNP
rs756308923 858 dbSNP
rs985275208 859 dbSNP
rs1381286294 860 dbSNP
rs912426584 861 dbSNP
rs913715736 865 dbSNP
rs1437687635 866 dbSNP
rs779247866 869 dbSNP
rs1467188314 873 dbSNP
rs1042349401 877 dbSNP
rs748573399 878 dbSNP
rs1426929867 881 dbSNP
rs1196226416 883 dbSNP
rs1468776902 888 dbSNP
rs551647719 892 dbSNP
rs560652078 893 dbSNP
rs1007182241 894 dbSNP
rs1038646583 897 dbSNP
rs1177447454 899 dbSNP
rs1305375995 904 dbSNP
rs1377995064 908 dbSNP
rs1422012237 919 dbSNP
rs531541151 920 dbSNP
rs1390392920 922 dbSNP
rs901619288 922 dbSNP
rs1403956555 923 dbSNP
rs997205251 925 dbSNP
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rs1460549479 930 dbSNP
rs1379551162 931 dbSNP
rs1177065548 934 dbSNP
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rs1454510109 940 dbSNP
rs1394243531 941 dbSNP
rs1054255154 947 dbSNP
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rs1012364798 950 dbSNP
rs1251215077 950 dbSNP
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rs4690194 953 dbSNP
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rs1242829902 964 dbSNP
rs150245247 965 dbSNP
rs906734185 965 dbSNP
rs770954216 967 dbSNP
rs547479027 968 dbSNP
rs1313627688 970 dbSNP
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rs1015179578 977 dbSNP
rs112899286 978 dbSNP
rs1171495039 980 dbSNP
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rs1364268265 984 dbSNP
rs1181004930 987 dbSNP
rs1280072369 988 dbSNP
rs1416731618 991 dbSNP
rs928594034 995 dbSNP
rs995195937 997 dbSNP
rs533041298 1006 dbSNP
rs1277776946 1007 dbSNP
rs988896862 1008 dbSNP
rs552842185 1016 dbSNP
rs571039099 1019 dbSNP
rs538565306 1021 dbSNP
rs114282746 1022 dbSNP
rs147538615 1023 dbSNP
rs535444932 1024 dbSNP
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rs1353740129 1026 dbSNP
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rs1402163875 1032 dbSNP
rs1385422761 1034 dbSNP
rs1451540058 1035 dbSNP
rs568003894 1037 dbSNP
rs978381737 1038 dbSNP
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rs1254873051 1046 dbSNP
rs1195410983 1052 dbSNP
rs554246041 1053 dbSNP
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rs1472128308 1064 dbSNP
rs1203792157 1068 dbSNP
rs572495069 1071 dbSNP
rs1274380453 1074 dbSNP
rs1232710745 1076 dbSNP
rs1332775836 1081 dbSNP
rs1419082616 1082 dbSNP
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rs1431738467 1086 dbSNP
rs1465253363 1090 dbSNP
rs1317345557 1100 dbSNP
rs1380335478 1103 dbSNP
rs539914242 1106 dbSNP
rs1165565756 1107 dbSNP
rs1047472126 1109 dbSNP
rs948111603 1110 dbSNP
rs187539726 1113 dbSNP
rs1006399685 1114 dbSNP
rs1333662459 1116 dbSNP
rs1241213046 1119 dbSNP
rs1191427628 1122 dbSNP
rs906660686 1126 dbSNP
rs1254104515 1127 dbSNP
rs575812903 1131 dbSNP
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rs940876766 1142 dbSNP
rs1491563877 1143 dbSNP
rs202121533 1143 dbSNP
rs1285696499 1144 dbSNP
rs1338927556 1149 dbSNP
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rs1217570834 1158 dbSNP
rs58212655 1160 dbSNP
rs1440072011 1161 dbSNP
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rs989339192 1164 dbSNP
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rs1165800005 1169 dbSNP
rs377592103 1170 dbSNP
rs969172671 1171 dbSNP
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rs540716341 1176 dbSNP
rs1205257635 1177 dbSNP
rs559288932 1179 dbSNP
rs1006589967 1183 dbSNP
rs1202379615 1186 dbSNP
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rs1303830916 1188 dbSNP
rs1233350688 1191 dbSNP
rs532916785 1193 dbSNP
rs974624856 1205 dbSNP
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rs1442218315 1210 dbSNP
rs1326350816 1220 dbSNP
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rs765012402 1223 dbSNP
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rs1375724618 1229 dbSNP
rs957969632 1230 dbSNP
rs551477307 1232 dbSNP
rs1410712718 1234 dbSNP
rs780849127 1234 dbSNP
rs1047818177 1236 dbSNP
rs1209845301 1236 dbSNP
rs1310227437 1236 dbSNP
rs1486106858 1236 dbSNP
rs1286194278 1240 dbSNP
rs916582273 1241 dbSNP
rs1277235669 1247 dbSNP
rs200807224 1247 dbSNP
rs756426966 1247 dbSNP
rs948038044 1247 dbSNP
rs1172041485 1248 dbSNP
rs1355652570 1249 dbSNP
rs550152390 1251 dbSNP
rs982158368 1251 dbSNP
rs191060812 1252 dbSNP
rs571623248 1252 dbSNP
rs1394163195 1259 dbSNP
rs868259715 1263 dbSNP
rs539141032 1266 dbSNP
rs1190091099 1268 dbSNP
rs899356713 1270 dbSNP
rs1399157733 1273 dbSNP
rs765848316 1278 dbSNP
rs1186095214 1281 dbSNP
rs1001818698 1282 dbSNP
rs1487007151 1282 dbSNP
rs567281504 1285 dbSNP
rs1316248129 1286 dbSNP
rs1050672748 1290 dbSNP
rs550506929 1293 dbSNP
rs1227758979 1297 dbSNP
rs889408135 1298 dbSNP
rs1234517633 1302 dbSNP
rs1334931827 1308 dbSNP
rs1292196419 1311 dbSNP
rs568615418 1314 dbSNP
rs896016388 1316 dbSNP
rs779944020 1321 dbSNP
rs1010245376 1322 dbSNP
rs1225719199 1323 dbSNP
rs182885031 1324 dbSNP
rs1020681565 1327 dbSNP
rs1258823926 1329 dbSNP
rs754930850 1337 dbSNP
rs968854693 1340 dbSNP
rs73058484 1341 dbSNP
rs1032170579 1343 dbSNP
rs964514295 1350 dbSNP
rs1265849916 1353 dbSNP
rs1429300836 1354 dbSNP
rs1198457257 1355 dbSNP
rs1271949912 1364 dbSNP
rs768506992 1364 dbSNP
rs1308840021 1370 dbSNP
rs1295885438 1374 dbSNP
rs900903983 1377 dbSNP
rs879756512 1378 dbSNP
rs1174409520 1384 dbSNP
rs1214286757 1387 dbSNP
rs1375977950 1389 dbSNP
rs1363488716 1391 dbSNP
rs1419073203 1392 dbSNP
rs999713228 1397 dbSNP
rs759798969 1398 dbSNP
rs923201693 1401 dbSNP
rs1323950128 1404 dbSNP
rs1463611322 1408 dbSNP
rs1030827620 1411 dbSNP
rs1355295341 1414 dbSNP
rs958150555 1415 dbSNP
rs1010784661 1420 dbSNP
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rs1195307403 1428 dbSNP
rs1454639528 1431 dbSNP
rs1252319171 1433 dbSNP
rs1023565116 1434 dbSNP
rs1207506300 1436 dbSNP
rs969347808 1439 dbSNP
rs1363852310 1443 dbSNP
rs907512813 1450 dbSNP
rs566050044 1454 dbSNP
rs147877423 1455 dbSNP
rs539573766 1461 dbSNP
rs1057286930 1469 dbSNP
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rs1393152976 1469 dbSNP
rs937494398 1469 dbSNP
rs1235836975 1478 dbSNP
rs1280485920 1481 dbSNP
rs927972878 1482 dbSNP
rs1215129139 1483 dbSNP
rs557794351 1487 dbSNP
rs972590898 1488 dbSNP
rs920768043 1489 dbSNP
rs930807126 1491 dbSNP
rs1420874370 1494 dbSNP
rs1176168462 1496 dbSNP
rs1481856638 1499 dbSNP
rs1282051662 1502 dbSNP
rs1211993411 1503 dbSNP
rs57003523 1505 dbSNP
rs1000277082 1506 dbSNP
rs1241800445 1513 dbSNP
rs1435188190 1523 dbSNP
rs71666332 1525 dbSNP
rs774615859 1525 dbSNP
rs528262156 1526 dbSNP
rs910824944 1528 dbSNP
rs1357562280 1530 dbSNP
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rs1040677042 1533 dbSNP
rs900870090 1536 dbSNP
rs1156799877 1544 dbSNP
rs536803379 1545 dbSNP
rs1170669118 1555 dbSNP
rs954671096 1557 dbSNP
rs1364363487 1560 dbSNP
rs983758568 1561 dbSNP
rs1259099389 1570 dbSNP
rs1471342968 1570 dbSNP
rs907565486 1580 dbSNP
rs555534301 1581 dbSNP
rs963370129 1587 dbSNP
rs573890171 1589 dbSNP
rs999281732 1594 dbSNP
rs1254469601 1600 dbSNP
rs1207310462 1607 dbSNP
rs1351962097 1610 dbSNP
rs1052616994 1614 dbSNP
rs1226575338 1619 dbSNP
rs1337051726 1622 dbSNP
rs893606840 1627 dbSNP
rs541300276 1640 dbSNP
rs937044525 1642 dbSNP
rs1383729359 1644 dbSNP
rs562580393 1644 dbSNP
rs140234000 1657 dbSNP
rs1319816774 1658 dbSNP
rs969274212 1661 dbSNP
rs1455134082 1662 dbSNP
rs1003489668 1672 dbSNP
rs1165060233 1673 dbSNP
rs188780110 1674 dbSNP
rs1035018374 1675 dbSNP
rs1366374147 1676 dbSNP
rs1447938612 1680 dbSNP
rs192662647 1680 dbSNP
rs1261570216 1682 dbSNP
rs145629578 1686 dbSNP
rs972133229 1688 dbSNP
rs920681333 1690 dbSNP
rs904736138 1693 dbSNP
rs184751229 1698 dbSNP
rs1039652768 1700 dbSNP
rs1437362142 1706 dbSNP
rs1318117751 1714 dbSNP
rs899947881 1715 dbSNP
rs188071577 1718 dbSNP
rs1396660529 1726 dbSNP
rs1030191271 1727 dbSNP
rs910751374 1729 dbSNP
rs1469965945 1741 dbSNP
rs1214585766 1742 dbSNP
rs1169295552 1744 dbSNP
rs755865645 1749 dbSNP
rs944953709 1751 dbSNP
rs531948214 1753 dbSNP
rs1237590924 1754 dbSNP
rs1456512080 1757 dbSNP
rs1040644672 1758 dbSNP
rs922254470 1763 dbSNP
rs1339024845 1766 dbSNP
rs550446730 1769 dbSNP
rs1225929810 1774 dbSNP
rs963256374 1775 dbSNP
rs1052161991 1776 dbSNP
rs767346052 1776 dbSNP
rs1378122422 1788 dbSNP
rs893565509 1791 dbSNP
rs1330382300 1794 dbSNP
rs62294081 1795 dbSNP
rs1369617402 1797 dbSNP
rs992570557 1799 dbSNP
rs1044905955 1804 dbSNP
rs905059447 1806 dbSNP
rs1462651522 1809 dbSNP
rs1396143844 1812 dbSNP
rs1191137621 1816 dbSNP
rs1003456998 1818 dbSNP
rs1477361085 1820 dbSNP
rs573601290 1822 dbSNP
rs1182682009 1824 dbSNP
rs946210559 1830 dbSNP
rs150674752 1832 dbSNP
rs993926480 1835 dbSNP
rs1349795981 1837 dbSNP
rs1280849827 1838 dbSNP
rs1218568099 1839 dbSNP
rs1342839302 1847 dbSNP
rs1280767103 1853 dbSNP
rs139866111 1854 dbSNP
rs539406149 1856 dbSNP
rs551463213 1858 dbSNP
rs1374659828 1861 dbSNP
rs1039705176 1864 dbSNP
rs1376432200 1865 dbSNP
rs986214095 1867 dbSNP
rs1017726545 1870 dbSNP
rs1413242223 1875 dbSNP
rs149802776 1882 dbSNP
rs145746716 1883 dbSNP
rs887159002 1884 dbSNP
rs1249814804 1887 dbSNP
rs1234068395 1888 dbSNP
rs924870622 1890 dbSNP
rs934988138 1892 dbSNP
rs1237804011 1896 dbSNP
rs1209226097 1900 dbSNP
rs1257659420 1907 dbSNP
rs1310320130 1911 dbSNP
rs1286302785 1921 dbSNP
rs191240491 1923 dbSNP
rs1014730338 1932 dbSNP
rs899099486 1933 dbSNP
rs994738984 1935 dbSNP
rs1355743667 1936 dbSNP
rs1302580880 1940 dbSNP
rs1446319893 1943 dbSNP
rs183828880 1944 dbSNP
rs1319568323 1945 dbSNP
rs946441402 1951 dbSNP
rs1233562628 1953 dbSNP
rs1034050317 1956 dbSNP
rs189426692 1957 dbSNP
rs1181228458 1958 dbSNP
rs553196385 1965 dbSNP
rs1255062409 1970 dbSNP
rs1181031246 1971 dbSNP
rs1243719321 1972 dbSNP
rs1482158491 1972 dbSNP
rs1209264717 1975 dbSNP
rs765779306 1975 dbSNP
rs904985916 1977 dbSNP
rs939172812 1982 dbSNP
rs182077358 1983 dbSNP
rs1894 1984 dbSNP
rs1422457898 1985 dbSNP
rs1321905676 2000 dbSNP
rs1311576070 2002 dbSNP
rs778483096 2002 dbSNP
rs978013485 2003 dbSNP
rs926108430 2004 dbSNP
rs1171869354 2007 dbSNP
rs185076832 2014 dbSNP
rs1387152591 2021 dbSNP
rs776098643 2022 dbSNP
rs575454089 2025 dbSNP
rs1349453002 2028 dbSNP
rs542729033 2028 dbSNP
rs1162968565 2031 dbSNP
rs1301620495 2032 dbSNP
rs887819802 2037 dbSNP
rs1421386825 2039 dbSNP
rs1189023554 2041 dbSNP
rs1415767478 2043 dbSNP
rs1448773029 2043 dbSNP
rs933994161 2044 dbSNP
rs1007560501 2045 dbSNP
rs1278016996 2047 dbSNP
rs1316258841 2048 dbSNP
rs752351646 2053 dbSNP
rs1264407211 2060 dbSNP
rs190366269 2061 dbSNP
rs966154473 2062 dbSNP
rs1363597619 2063 dbSNP
rs976674965 2064 dbSNP
rs1031861424 2065 dbSNP
rs62294082 2066 dbSNP
rs1463694577 2070 dbSNP
rs1355388240 2071 dbSNP
rs770407021 2072 dbSNP
rs139523133 2073 dbSNP
rs946366376 2074 dbSNP
rs559948985 2076 dbSNP
rs181767657 2077 dbSNP
rs759433107 2080 dbSNP
rs76817730 2081 dbSNP
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rs76358337 2083 dbSNP
rs1204807123 2084 dbSNP
rs1340503561 2085 dbSNP
rs998604993 2092 dbSNP
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rs1234599019 2111 dbSNP
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rs567362437 2119 dbSNP
rs975512420 2120 dbSNP
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rs1174143182 2129 dbSNP
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rs1377019153 2134 dbSNP
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rs534777303 2170 dbSNP
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rs760480028 2188 dbSNP
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rs1445082244 2213 dbSNP
rs956270718 2215 dbSNP
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rs561521894 2246 dbSNP
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rs771507500 2260 dbSNP
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rs1209464385 2281 dbSNP
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rs909151899 2298 dbSNP
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rs1296789755 2301 dbSNP
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rs1284742448 2321 dbSNP
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rs559510760 2390 dbSNP
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rs950040753 2399 dbSNP
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rs1013272063 2681 dbSNP
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rs950483886 2696 dbSNP
rs180817173 2701 dbSNP
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rs1374795712 2714 dbSNP
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rs1374745289 2724 dbSNP
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rs1330008229 2757 dbSNP
rs759111142 2758 dbSNP
rs974597067 2760 dbSNP
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rs988807178 2783 dbSNP
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rs565844068 2791 dbSNP
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rs990019160 2797 dbSNP
rs1213670239 2806 dbSNP
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rs1281420583 2817 dbSNP
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rs1188745987 2823 dbSNP
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rs878932685 2827 dbSNP
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rs185266110 2843 dbSNP
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rs1245284521 2859 dbSNP
rs1358559532 2860 dbSNP
rs1312850753 2861 dbSNP
rs575553725 2862 dbSNP
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rs879208146 2864 dbSNP
rs1429385365 2865 dbSNP
rs1380151750 2867 dbSNP
rs1198209353 2871 dbSNP
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rs559444101 4901 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- 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.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 10336.0
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... "PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000362003.5 | 3UTR | AAUAAAUAUUACCUGUCUACCUCAAAAUACAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000362003.5 | 3UTR | AAUAAAUAUUACCUGUCUACCUCAAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000362003.5 | 3UTR | AAUAAAUAUUACCUGUCUACCUCAAAAUACACAUACUGCUGAAGCAUUCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE28260 Renal cortex and medulla 0.691 4.5e-3 0.725 2.5e-3 13 Click to see details
GSE28544 Breast cancer 0.399 2.7e-2 0.367 3.9e-2 24 Click to see details
GSE32688 Pancreatic cancer 0.276 6.3e-2 0.261 7.5e-2 32 Click to see details