SomamiR DB

SomamiR DB 2.0 Somatic mutations altering microRNA-ceRNA interactions
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Prediction criteria:	TargetScan sites only All 6mer or longer seed matches

PolymiRTS Database

RefSeq ID:	NM_001253388
Gene Symbol:	CHL1
Description:	Homo sapiens cell adhesion molecule with homology to L1CAM (close homolog of L1) (CHL1), transcript variant 2, mRNA.
Browse Associations

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.406280T>C			COSN15169062		LP6005690-DNA_F02		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3065-5p	tagtaTTTGTTGAgctcct	0	UCAACAAA	m8a	Disrupted	-0.057000	0.042000	2.190000
hsa-miR-545-3p	tagtaTTTGCTGAgctcct	0	UCAGCAAA	m8a	Created	no TS	-0.176000	-3.230000
hsa-miR-7-1-3p	tagtATTTGTTGagctcct	0	CAACAAAU	m8a	Disrupted	0.061000	0.034000	No effect
hsa-miR-7-2-3p	tagtATTTGTTGagctcct	0	CAACAAAU	m8a	Disrupted	0.061000	0.034000	0.010000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.406285C>T			COSN5536513		RK143_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-28-5p	tttgttgAGCTCCTatttg	0	AAGGAGCU	m7b	Disrupted	-0.308000	no TS	2.000000
hsa-miR-3139	tttgttgAGCTCCTAtttg	0	UAGGAGCU	m8a	Disrupted	-0.329000	no TS	2.270000
hsa-miR-3670	tttgtTGAGCTCctatttg	0	AGAGCUCA	m7b	Disrupted	-0.176000	no TS	0.010000
hsa-miR-3914	tttgttgaGTTCCTatttg	0	AAGGAACC	m6b	Created	-0.132000	-0.236000	No effect
hsa-miR-4633-3p	tttgttgAGCTCCTatttg	0	AGGAGCUA	m7a	Disrupted	-0.019000	-0.019000	0.160000
hsa-miR-708-5p	tttgttgAGCTCCTatttg	0	AAGGAGCU	m7b	Disrupted	-0.319000	no TS	2.250000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.406466C>T			COSN6768674		RK308_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.406857A>G			COSN1950621		RK075_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4446-5p	tattgAGGGAAATgttttc	0	AUUUCCCU	m8a	Disrupted	-0.055000	0.015000	No effect
hsa-miR-543	tattgagggGAATGTTTtc	0	AAACAUUC	m8a	(m7b->m8a)	-0.037000	-0.002000	-0.010000
hsa-miR-642a-5p	tattGAGGGAaatgttttc	0	GUCCCUCU	m6b	Disrupted	-0.115000	no TS	0.030000
hsa-miR-4446-5p	tattgAGGGAAATgttttc	0	AUUUCCCU	m8a	Disrupted	-0.055	0.015	No effect
hsa-miR-543	tattgagggGAATGTTTtc	0	AAACAUUC	m8a	(m7b->m8a)	-0.037	-0.002	-0.01
hsa-miR-642a-5p	tattGAGGGAaatgttttc	0	GUCCCUCU	m6b	Disrupted	-0.115	no TS	0.03

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.406951C>A			COSN9551938		AOCS-094-1-1		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4307	aaattcctAAACATacgtt	0	AAUGUUUU	m6b	Created	-0.106000	0.013000	No effect
hsa-miR-567	aaattcctaAACATACgtt	0	AGUAUGUU	m7b	(m6c->m7b)	no TS	-0.033000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407093G>A			COSN5536519		RK043_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1206	attgtaCATGAACAtgttt	0	UGUUCAUG	m8a	Disrupted	-0.094000	-0.018000	0.610000
hsa-miR-3924	attgTACATAaacatgttt	0	AUAUGUAU	m6b	Created	0.005000	0.075000	-2.180000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407210G>A			COSN6768688		RK077_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-302a-5p	actGTTTAAGTgaattgac	0	ACUUAAAC	m8a	Disrupted	0.066000	no TS	0.270000
hsa-miR-4729	actgttTAAATGAattgac	0	UCAUUUAU	m7a	Created	no TS	0.139000	-0.030000
hsa-miR-4760-3p	actgtttaaATGAATTgac	0	AAAUUCAU	m7b	(m6c->m7b)	-0.030000	0.042000	No effect
hsa-miR-5696	actgttTAAATGAattgac	0	CUCAUUUA	m7b	Created	0.097000	0.241000	-0.050000
hsa-miR-664-3p	actgtttaAATGAATtgac	0	UAUUCAUU	m7b	Created	0.034000	0.096000	-0.030000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407466G>T			COSN5003226		SS6003125		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1247-3p	cgcagTCCCGGGagtaagc	0	CCCCGGGA	m7b	Disrupted	-0.149000	no TS	5.040000
hsa-miR-211-3p	cgcaGTCCCTGgagtaagc	0	GCAGGGAC	m7b	Created	no TS	-0.003000	No effect
hsa-miR-3145-5p	cgcagtcccTGGAGTaagc	0	AACUCCAA	m6b	Created	no TS	0.039000	-1.650000
hsa-miR-3199	cgCAGTCCCTggagtaagc	0	AGGGACUG	m8a	(m7a->m8a)	0.056000	0.029000	0.080000
hsa-miR-3925-3p	cgcagtccCTGGAGTaagc	0	ACUCCAGU	m7a	Created	NA	NA	-0.080000
hsa-miR-4532	cgcagtCCCGGGagtaagc	0	CCCCGGGG	m6b	Disrupted	-0.078000	no TS	5.720000
hsa-miR-4685-5p	cgcagtCCCTGGagtaagc	0	CCCAGGGC	m6b	Created	no TS	0.004000	-2.430000
hsa-miR-508-5p	cgcagtccCTGGAGTAagc	0	UACUCCAG	m8a	Created	no TS	0.040000	-1.090000
hsa-miR-766-3p	cgcagtccCTGGAGTaagc	0	ACUCCAGC	m7a	Created	NA	NA	-1.270000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407687G>T			COSN9551956		AOCS-144-1-3		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-21-3p	agttcTGGTGTTattctgt	0	CAACACCA	m7b	Disrupted	-0.132000	-0.182000	3.030000
hsa-miR-3591-3p	agttcTGGTGTTattctgt	0	AAACACCA	m7b	Disrupted	-0.151000	-0.201000	5.660000
hsa-miR-548aa	agttcTGGTTTTattctgt	0	AAAAACCA	m7b	Created	0.035000	0.216000	-2.260000
hsa-miR-548ap-3p	agttcTGGTTTTattctgt	0	AAAAACCA	m7b	Created	0.035000	0.216000	-0.690000
hsa-miR-548at-3p	agttctGGTTTTattctgt	0	CAAAACCG	m6b	Created	-0.032000	0.048000	-0.060000
hsa-miR-548t-3p	agttcTGGTTTTattctgt	0	AAAAACCA	m7b	Created	0.035000	0.216000	-2.260000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407748G>T			COSN6768703		RK028_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-490-3p	agtcatgCAGGTTagaaat	0	CAACCUGG	m6b	Disrupted	-0.113000	-0.101000	0.040000
hsa-miR-649	agtcatgCAGGTTagaaat	0	AAACCUGU	m6b	Disrupted	-0.515000	-0.507000	0.020000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407789T>G			COSN7698943		8066491		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-154-5p	ttaATAACCTttaagtcag	0	UAGGUUAU	m7b	(m7b->m6b)	-0.123000	-0.056000	0.010000
hsa-miR-548m	ttaataACCTTTaagtcag	0	CAAAGGUA	m6b	Disrupted	-0.180000	-0.215000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.407922T>C			COSN1950645		RK027_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-216a	tatgaaaaaTGAGATTgaa	0	UAAUCUCA	m7b	(m7b->m6c)	-0.003000	no TS	0.860000
hsa-miR-5696	tatgaaAAATGAGattgaa	0	CUCAUUUA	m7a	Disrupted	0.097000	0.097000	0.140000
hsa-miR-216a	tatgaaaaaTGAGATTgaa	0	UAAUCUCA	m7b	(m7b->m6c)	-0.003	no TS	0.86
hsa-miR-5696	tatgaaAAATGAGattgaa	0	CUCAUUUA	m7a	Disrupted	0.097	0.097	0.14

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.408012T>C			COSN1950648		RK031_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-26a-1-3p	caaaagGAATAGatctatg	0	CCUAUUCU	m6b	Disrupted	-0.053000	-0.100000	0.030000
hsa-miR-26a-2-3p	caaaagGAATAGatctatg	0	CCUAUUCU	m6b	Disrupted	-0.053000	-0.100000	0.040000
hsa-miR-26b-3p	caaaagGAACAGatctatg	0	CCUGUUCU	m6b	Created	-0.197000	-0.179000	-1.780000
hsa-miR-26a-1-3p	caaaagGAATAGatctatg	0	CCUAUUCU	m6b	Disrupted	-0.053	-0.1	0.03
hsa-miR-26a-2-3p	caaaagGAATAGatctatg	0	CCUAUUCU	m6b	Disrupted	-0.053	-0.1	0.04
hsa-miR-26b-3p	caaaagGAACAGatctatg	0	CCUGUUCU	m6b	Created	-0.197	-0.179	-1.78

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.408020T>A			COSN6768712		RK207_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-376a-3p	atagaTCTATGATtgaccc	0	AUCAUAGA	m8a	Disrupted	-0.022000	no TS	1.180000
hsa-miR-376b	atagaTCTATGATtgaccc	0	AUCAUAGA	m8a	Disrupted	-0.022000	no TS	1.540000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.409059T>G			COSN9551980		AOCS-141-3-2		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-200a-5p	ccatTAAGATatgattcat	0	CAUCUUAC	m6b	Disrupted	-0.124000	-0.069000	No effect
hsa-miR-200b-5p	ccatTAAGATatgattcat	0	CAUCUUAC	m6b	Disrupted	-0.132000	-0.080000	0.200000
hsa-miR-3675-3p	ccattaAGAGATGattcat	0	CAUCUCUA	m7a	Created	-0.048000	-0.048000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.409061T>C			COSN5044754		HX35T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-15b-3p	attaagatATGATTCatgt	0	CGAAUCAU	m7b	Disrupted	-0.317000	-0.061000	No effect
hsa-miR-5686	attaagATACGATtcatgt	0	UAUCGUAU	m7b	Created	no TS	-0.253000	-1.610000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.409122T>C			COSN9720955		C0021T		[kidney][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-190a	gtggtagtACATATCctag	0	UGAUAUGU	m7b	Created	no TS	-0.139000	No effect
hsa-miR-190b	gtggtagtACATATCctag	0	UGAUAUGU	m7b	Created	no TS	-0.139000	No effect
hsa-miR-3201	gtggtagtaCATATCCtag	0	GGGAUAUG	m7b	(m6c->m7b)	no TS	-0.175000	No effect
hsa-miR-4791	gtggtagtaCATATCCtag	0	UGGAUAUG	m7b	(m6c->m7b)	no TS	-0.212000	-0.060000
hsa-miR-5011-5p	gtggtagTATATATcctag	0	UAUAUAUA	m7b	Disrupted	0.045000	no TS	2.180000

Mutation			Mutation ID		Sample Name		Cancer Type
chr3:g.409354A>G			COSN6768733		RK178_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

**Germline mutations in target sites of miRNAs in somatic mutation table**
Location	SNP ID	Ancestral Allele	Allele	miR ID	Conservation	miRSite	FuncClass	Validation	context+ score change
405798	rs112733005	A	A	hsa-miR-26a-1-3p hsa-miR-26a-2-3p hsa-miR-4482-3p hsa-miR-6731-3p hsa-miR-7159-3p	0	agGAATAGAaaca agGAATAGAaaca aggAATAGAAAca aGGAATAGAaaca aggaATAGAAAca	Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N	-0.1 -0.1 -0.096 -0.357 -0.01
405798	rs112733005	A	G	hsa-miR-587	0	aggaATGGAAAca	Created	N	-0.062
406164	rs181398902	A
406164	rs181398902	A	G	hsa-miR-302a-5p	0	aTTTAAGAtgtaa	Created	N	0.016
406373	rs186877363	C	C	hsa-miR-3691-5p hsa-miR-4764-5p	0	ttatgaCATCCAC ttatgACATCCAc	Disrupted Disrupted	N N	-0.205 -0.1
406373	rs186877363	C	T	hsa-miR-144-5p hsa-miR-154-3p hsa-miR-3201 hsa-miR-376b-5p hsa-miR-376c-5p hsa-miR-4791 hsa-miR-487a-3p	0	ttaTGATATCcac tTATGATAtccac ttatgATATCCAc ttatgaTATCCAC ttatgaTATCCAC ttatgATATCCAc tTATGATAtccac	Created Created Created Created Created Created Created	N N N N N N N	-0.13 -0.005 -0.068 -0.158 -0.158 -0.085 -0.012
407051	rs115293529	A	A	hsa-miR-10a-3p	0	GAATTTAttttct	Disrupted	N	0.112
407051	rs115293529	A	G	hsa-miR-570-3p hsa-miR-7-1-3p hsa-miR-7-2-3p	0	gaattTGTTTTCt gaATTTGTTttct gaATTTGTTttct	Created Created Created	N N N	0.07 0.143 0.152
407398	rs60386302	G	G	hsa-miR-1284 hsa-miR-181a-5p hsa-miR-181b-5p hsa-miR-181c-5p hsa-miR-181d-5p hsa-miR-4262	0	cagaaTGTATAGA caGAATGTAtaga caGAATGTAtaga caGAATGTAtaga caGAATGTAtaga caGAATGTAtaga	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N HT N N N N	0.026 0.101 0.101 0.097 0.101 0.104
407398	rs60386302	G	A	hsa-miR-190a-3p hsa-miR-4778-5p hsa-miR-5011-5p hsa-miR-6074	0	cagaATATATAga CAGAATAtataga cagaATATATAga caGAATATAtaga	Created Created Created Created	N N N N	0.196 0.072 0.216 0.144
407461	rs149309897	G	G	hsa-miR-1288-3p hsa-miR-3199 hsa-miR-8052	0	accGCAGTCCcgg accgCAGTCCCgg accgCAGTCCCgg	Disrupted Disrupted Disrupted	N N N	0.001 0.056 0.056
407461	rs149309897	G
407467	rs145455412	G	G	hsa-miR-1247-3p hsa-miR-4532	0	gTCCCGGGAgtaa gtCCCGGGAgtaa	Disrupted Disrupted	N N	-0.149 -0.078
407467	rs145455412	G	T	hsa-miR-3680-5p hsa-miR-4798-3p	0	gtcccGTGAGTAa gtccCGTGAGTAa	Created Created	N N	0.04 0.006
407880	rs3931062	A	G	hsa-miR-1199-5p hsa-miR-4303 hsa-miR-4468 hsa-miR-4722-5p hsa-miR-6165 hsa-miR-6751-3p	0	gctcctGCTCAGA gctcctGCTCAGA gctcCTGCTCAga gCTCCTGCtcaga gcTCCTGCTcaga gctcctGCTCAGA	Created Created Created Created Created Created	N N N N N N	0.013 -0.03 0.006 -0.013 0.04 0.007
407880	rs3931062	A	A	hsa-miR-28-5p hsa-miR-3139 hsa-miR-4682 hsa-miR-6869-5p hsa-miR-708-5p	0	GCTCCTActcaga GCTCCTActcaga gctcctACTCAGA gctcCTACTCAga GCTCCTActcaga	Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N	-0.029 -0.036 0.029 0.041 -0.039
408343	rs75253951	T	T	hsa-miR-3914	0	catgaGTTCCTAg	Disrupted	N	-0.003
408343	rs75253951	T	C	hsa-miR-28-5p hsa-miR-3139 hsa-miR-3670 hsa-miR-6847-3p hsa-miR-708-5p	0	catgAGCTCCTAg catgAGCTCCTAg caTGAGCTCctag CATGAGCtcctag catgAGCTCCTAg	Created Created Created Created Created	N N N N N	-0.096 -0.117 -0.05 0.008 -0.107
408591	rs148621138	G
408591	rs148621138	G	A	hsa-miR-410-3p hsa-miR-5011-5p	0	aaTTATATAtctg aatTATATATctg	Created Created	N N	0.087 0.066
409298	rs75434206	G
409298	rs75434206	G	A	hsa-miR-4307	0	tAAAACATgtttg	Created	N	-0.134
409368	rs150917959	C	C	hsa-miR-568 hsa-miR-6516-3p	0	aTTATACAtgaaa attaTACATGAAa	Disrupted Disrupted	N N	-0.189 -0.378
409368	rs150917959	C	T	hsa-miR-410-3p hsa-miR-5007-3p hsa-miR-5011-5p	0	aTTATATAtgaaa attatATATGAAa atTATATATgaaa	Created Created Created	N N N	-0.015 -0.109 -0.101

**Genome Browser**
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Somatic mutations that impact miRNA target sites

Germline mutations in target sites of miRNAs in somatic mutation table

Genome Browser