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_000376
Gene Symbol:	VDR
Description:	Homo sapiens vitamin D (1,25- dihydroxyvitamin D3) receptor (VDR), transcript variant 1, mRNA.
Gene Location:	chr12(-):48235319-48298814
Browse Associations

Mutation			Mutation ID		Sample Name		Cancer Type
chr12:g.47842120C>T			COSN5796329		EOPC-010_tumor		[prostate][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1253	accacCTTCTCagctctcc	2	AGAGAAGA	m6b	Created	0.029000	0.026000	-2.690000
hsa-miR-204-3p	accaccTTCCCAGCtctcc	2	GCUGGGAA	m8a	Disrupted	-0.307000	-0.288000	1.410000
hsa-miR-3160-3p	accaccttcTCAGCTCTcc	0	AGAGCUGA	m8a	(m7a->m8a)	no TS	-0.071000	-0.900000
hsa-miR-4251	accaccTTCTCAGctctcc	4	CCUGAGAA	m7b	Created	0.033000	0.048000	-0.030000
hsa-miR-4487	accaccttcCCAGCTCTcc	6	AGAGCUGG	m8a	(m8a->m7a)	-0.130000	no TS	0.440000
hsa-miR-4646-5p	accaccTTCCCAGctctcc	2	ACUGGGAA	m7b	Disrupted	-0.306000	-0.278000	0.250000
hsa-miR-4747-5p	accaCCTTCCCagctctcc	1	AGGGAAGG	m7b	Disrupted	-0.378000	-0.164000	0.010000
hsa-miR-5196-5p	accaCCTTCCCagctctcc	1	AGGGAAGG	m7b	Disrupted	-0.397000	-0.183000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr12:g.47842714G>T			COSN9562075		AOCS-155-3-5		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4714-3p	gaggTAGGTTGatcacctg	0	CCAACCUA	m7b	Created	no TS	0.032000	-0.030000
hsa-miR-640	gaggtaggTGGATCAcctg	1	AUGAUCCA	m7b	Disrupted	0.093000	0.060000	0.110000

Mutation			Mutation ID		Sample Name		Cancer Type
chr12:g.47842735G>C			ICGC_8616A8CA-2A78-11E2-96E7-04FD496BB9B8		CPCG_0102_Pr_P_P1		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-106a-5p	atcccaGCACTTTgggagg	0	AAAAGUGC	m7b	Created	no TS	0.096	-0.01
hsa-miR-106b-5p	atcccaGCACTTTgggagg	0	UAAAGUGC	m7b	Created	no TS	0.115	No effect
hsa-miR-17-5p	atcccaGCACTTTGggagg	0	CAAAGUGC	m8a	Created	no TS	0.096	-0.01
hsa-miR-186-3p	atcccagcaCTTTGGGagg	0	GCCCAAAG	m7b	(m6b->m7b)	0.081	0.043	-0.04
hsa-miR-20a-5p	atcccaGCACTTTgggagg	0	UAAAGUGC	m7b	Created	no TS	0.106	No effect
hsa-miR-20b-5p	atcccaGCACTTTGggagg	0	CAAAGUGC	m8a	Created	no TS	0.106	-0.01
hsa-miR-302a-3p	atcccAGCACTTtgggagg	0	UAAGUGCU	m7b	Created	-0.384	-0.277	No effect
hsa-miR-302b-3p	atcccAGCACTTtgggagg	0	UAAGUGCU	m7b	Created	-0.384	-0.277	No effect
hsa-miR-302c-3p	atcccAGCACTTtgggagg	0	UAAGUGCU	m7b	Created	-0.384	-0.277	No effect
hsa-miR-302d-3p	atcccAGCACTTtgggagg	0	UAAGUGCU	m7b	Created	-0.384	-0.277	No effect
hsa-miR-302e	atcccAGCACTTtgggagg	0	UAAGUGCU	m7b	Created	-0.374	-0.258	No effect
hsa-miR-3692-5p	atcCCAGCAGtttgggagg	0	CCUGCUGG	m7b	(m7b->m6c)	-0.022	no TS	0.11
hsa-miR-372	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.395	-0.307	No effect
hsa-miR-373-3p	atcccAGCACTTtgggagg	0	GAAGUGCU	m7b	Created	-0.374	-0.286	No effect
hsa-miR-512-3p	atccCAGCACTTtgggagg	0	AAGUGCUG	m8a	Created	no TS	0.04	No effect
hsa-miR-519d	atcccaGCACTTTGggagg	0	CAAAGUGC	m8a	Created	no TS	0.096	8.26
hsa-miR-520a-3p	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.374	-0.267	No effect
hsa-miR-520b	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.384	-0.296	No effect
hsa-miR-520c-3p	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.384	-0.296	No effect
hsa-miR-520d-3p	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.374	-0.267	No effect
hsa-miR-520e	atcccAGCACTTTgggagg	0	AAAGUGCU	m8a	Created	-0.395	-0.288	No effect
hsa-miR-520g	atcccagCACTTTGggagg	0	ACAAAGUG	m7b	Created	no TS	0.152	-0.03
hsa-miR-520h	atcccagCACTTTGggagg	0	ACAAAGUG	m7b	Created	no TS	0.152	No effect
hsa-miR-526b-3p	atcccaGCACTTTgggagg	0	GAAAGUGC	m7b	Created	no TS	0.096	No effect
hsa-miR-548av-3p	atcccaGCAGTTTgggagg	0	AAAACUGC	m7b	Disrupted	0.083	no TS	No effect
hsa-miR-93-5p	atcccaGCACTTTGggagg	0	CAAAGUGC	m8a	Created	no TS	0.106	-0.09

Mutation			Mutation ID		Sample Name		Cancer Type
chr12:g.47843188T>G			COSN9562076		AOCS-096-1-7		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4251	ccatgtcTCTCAGaattct	4	CCUGAGAA	m6b	Disrupted	0.033000	no TS	6.590000
hsa-miR-4329	ccatgtcTCTCAGaattct	4	CCUGAGAC	m6b	Disrupted	0.041000	no TS	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr12:g.47843312A>G			COSN5945151		RK308_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1260a	gtcaGTGGGAacgtgactg	4	AUCCCACC	m6b	Disrupted	-0.128000	-0.145000	No effect
hsa-miR-1260b	gtcaGTGGGAacgtgactg	4	AUCCCACC	m6b	Disrupted	-0.122000	-0.139000	0.010000
hsa-miR-188-3p	gtcaGTGGGAacgtgactg	4	CUCCCACA	m6b	Disrupted	-0.038000	-0.056000	2.550000
hsa-miR-3156-3p	gtcAGTGGGAacgtgactg	2	CUCCCACU	m7b	(m7b->m6c)	0.002000	-0.008000	No effect
hsa-miR-4286	gtcAGTGGGGacgtgactg	0	ACCCCACU	m7b	(m6c->m7b)	-0.296000	-0.332000	-3.080000
hsa-miR-4301	gtcAGTGGGAacgtgactg	0	UCCCACUA	m7a	(m7a->m6b)	-0.130000	-0.096000	0.810000

**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
47841996	rs186085433	A	A	hsa-miR-627-3p hsa-miR-6795-3p hsa-miR-6826-3p hsa-miR-6887-3p	2 1 1 1	GAAAAGAggggaa gaaaaGAGGGGAa gaaaaGAGGGGAA gaaaaGAGGGGAa	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.034 -0.21 -0.461 -0.195
47841996	rs186085433	A	T	hsa-miR-2355-5p hsa-miR-4286 hsa-miR-5003-3p	1 1 2	gaaaagTGGGGAA gaaaAGTGGGGAa GAAAAGTggggaa	Created Created Created	N N N	-0.134 -0.397 -0.018
47842305	rs180727640	C	C	hsa-miR-1252-5p hsa-miR-4533 hsa-miR-4747-5p hsa-miR-5196-5p hsa-miR-7113-5p	5 7 5 5 6	TTCCTTCcctggc tTCCTTCCctggc ttCCTTCCCtggc ttCCTTCCCtggc ttcctTCCCTGGc	Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N	0.056 -0.026 -0.119 -0.138 -0.117
47842305	rs180727640	C
47842730	rs191342557	G	G	hsa-miR-150-5p hsa-miR-186-3p	2 2	agtTTGGGAGgtc agTTTGGGAggtc	Disrupted Disrupted	N N	0.032 0.081
47842730	rs191342557	G	A	hsa-miR-371a-5p hsa-miR-371b-5p hsa-miR-372-5p hsa-miR-373-5p hsa-miR-616-5p hsa-miR-6800-3p hsa-miR-6821-3p	1 2 2 2 2 1 1	aGTTTGAGAggtc agTTTGAGAggtc agTTTGAGAggtc agTTTGAGAggtc agTTTGAGAggtc agtttGAGAGGTc agtttgAGAGGTC	Created Created Created Created Created Created Created	N N N N N N N	0.098 0.137 0.135 0.134 0.144 -0.032 0.006
47842881	rs11540149	G	G	hsa-miR-150-5p hsa-miR-2116-3p hsa-miR-4713-5p hsa-miR-532-3p hsa-miR-629-3p hsa-miR-6867-3p	3 3 3 3 3 3	gTGGGAGAaaaca gTGGGAGAaaaca gTGGGAGAAaaca GTGGGAGAaaaca gtGGGAGAAAaca gtGGGAGAAaaca	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	-0.012 -0.047 -0.055 -0.15 -0.071 -0.019
47842881	rs11540149	G	A	hsa-miR-1260a hsa-miR-1260b hsa-miR-188-3p hsa-miR-3156-3p hsa-miR-4446-5p	3 3 3 3 3	GTGGGAAaaaaca GTGGGAAaaaaca GTGGGAAaaaaca GTGGGAAaaaaca gtGGGAAAAaaca	Created Created Created Created Created	N N N N N	-0.031 -0.031 -0.034 -0.062 0.053
47844184	rs3858733	A	A	hsa-miR-4747-5p hsa-miR-5196-5p	1 1	CTTCCCAtcactg CTTCCCAtcactg	Disrupted Disrupted	N N	-0.045 -0.045
47844184	rs3858733	A	C	hsa-miR-1914-3p hsa-miR-3184-5p hsa-miR-423-5p hsa-miR-4271 hsa-miR-4725-3p hsa-miR-5194 hsa-miR-6734-5p hsa-miR-6738-5p hsa-miR-6780b-5p hsa-miR-6783-5p	1 1 1 1 1 1 1 1 1 1	cttCCCCTCActg cttCCCCTCActg cttCCCCTCActg CTTCCCCtcactg CTTCCCCtcactg cttCCCCTCActg cttCCCCTCActg cttCCCCTCActg CTTCCCCtcactg cTTCCCCTcactg	Created Created Created Created Created Created Created Created Created Created	N N N N N N N N N N	-0.121 -0.119 -0.112 -0.142 -0.142 -0.124 -0.167 -0.124 -0.142 -0.077

**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