rs17755717

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

NTRK3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0125 (3753/29938,GnomAD)
A=0129 (3759/29118,TOPMED)
A=0109 (544/5008,1000G)
A=0176 (679/3854,ALSPAC)
A=0177 (656/3708,TWINSUK)

Position: chr15:88081865 (GRCh38.p7) (15q25.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 289 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.88081865G>A
GRCh37.p13 chr 15	NC_000015.9:g.88625096G>A
NTRK3 RefSeqGene	NG_029619.1:g.179867C>T

Gene: NTRK3, neurotrophic receptor tyrosine kinase 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NTRK3 transcript variant 3	NM_001007156.2:c.	N/A	Intron Variant
NTRK3 transcript variant 1	NM_001012338.2:c.	N/A	Intron Variant
NTRK3 transcript variant 4	NM_001243101.1:c.	N/A	Intron Variant
NTRK3 transcript variant 5	NM_001320134.1:c.	N/A	Intron Variant
NTRK3 transcript variant 6	NM_001320135.1:c.	N/A	Intron Variant
NTRK3 transcript variant 2	NM_002530.3:c.	N/A	Intron Variant
NTRK3 transcript variant X1	XM_006720543.3:c.	N/A	Intron Variant
NTRK3 transcript variant X4	XM_006720544.3:c.	N/A	Intron Variant
NTRK3 transcript variant X11	XM_006720545.3:c.	N/A	Intron Variant
NTRK3 transcript variant X16	XM_006720548.3:c.	N/A	Intron Variant
NTRK3 transcript variant X17	XM_006720549.3:c.	N/A	Intron Variant
NTRK3 transcript variant X18	XM_006720550.3:c.	N/A	Intron Variant
NTRK3 transcript variant X12	XM_011521637.2:c.	N/A	Intron Variant
NTRK3 transcript variant X21	XM_011521638.2:c.	N/A	Intron Variant
NTRK3 transcript variant X2	XM_017022240.1:c.	N/A	Intron Variant
NTRK3 transcript variant X5	XM_017022241.1:c.	N/A	Intron Variant
NTRK3 transcript variant X6	XM_017022242.1:c.	N/A	Intron Variant
NTRK3 transcript variant X7	XM_017022243.1:c.	N/A	Intron Variant
NTRK3 transcript variant X8	XM_017022244.1:c.	N/A	Intron Variant
NTRK3 transcript variant X9	XM_017022245.1:c.	N/A	Intron Variant
NTRK3 transcript variant X10	XM_017022246.1:c.	N/A	Intron Variant
NTRK3 transcript variant X13	XM_017022247.1:c.	N/A	Intron Variant
NTRK3 transcript variant X14	XM_017022248.1:c.	N/A	Intron Variant
NTRK3 transcript variant X15	XM_017022249.1:c.	N/A	Intron Variant
NTRK3 transcript variant X22	XM_017022251.1:c.	N/A	Intron Variant
NTRK3 transcript variant X23	XM_017022252.1:c.	N/A	Intron Variant
NTRK3 transcript variant X24	XM_017022253.1:c.	N/A	Intron Variant
NTRK3 transcript variant X25	XM_017022254.1:c.	N/A	Intron Variant
NTRK3 transcript variant X19	XM_017022250.1:c.	N/A	Genic Downstream Transcript Variant
NTRK3 transcript variant X3	XR_001751292.1:n.	N/A	Intron Variant
NTRK3 transcript variant X20	XR_001751293.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.933	A=0.067
1000Genomes	American	Sub	694	G=0.840	A=0.160
1000Genomes	East Asian	Sub	1008	G=0.938	A=0.062
1000Genomes	Europe	Sub	1006	G=0.842	A=0.158
1000Genomes	Global	Study-wide	5008	G=0.891	A=0.109
1000Genomes	South Asian	Sub	978	G=0.870	A=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.824	A=0.176
The Genome Aggregation Database	African	Sub	8718	G=0.923	A=0.077
The Genome Aggregation Database	American	Sub	836	G=0.860	A=0.140
The Genome Aggregation Database	East Asian	Sub	1620	G=0.959	A=0.041
The Genome Aggregation Database	Europe	Sub	18462	G=0.846	A=0.153
The Genome Aggregation Database	Global	Study-wide	29938	G=0.874	A=0.125
The Genome Aggregation Database	Other	Sub	302	G=0.830	A=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.870	A=0.129
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.823	A=0.177

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs17755717	0.000978	alcohol dependence	20201924

eQTL of rs17755717 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs17755717 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr15	88578742	88579073	E067	-46023
chr15	88579396	88580245	E067	-44851
chr15	88592917	88592971	E067	-32125
chr15	88593136	88593202	E067	-31894
chr15	88594306	88594356	E067	-30740
chr15	88594539	88594605	E067	-30491
chr15	88602124	88602199	E067	-22897
chr15	88602206	88602632	E067	-22464
chr15	88602642	88602692	E067	-22404
chr15	88602730	88602889	E067	-22207
chr15	88604669	88604987	E067	-20109
chr15	88612519	88612573	E067	-12523
chr15	88612794	88613304	E067	-11792
chr15	88620449	88620692	E067	-4404
chr15	88620789	88621310	E067	-3786
chr15	88633203	88634870	E067	8107
chr15	88670051	88670632	E067	44955
chr15	88670729	88670967	E067	45633
chr15	88671149	88671252	E067	46053
chr15	88577290	88577339	E068	-47757
chr15	88577645	88577699	E068	-47397
chr15	88577941	88577991	E068	-47105
chr15	88578008	88578099	E068	-46997
chr15	88578110	88578160	E068	-46936
chr15	88578370	88578681	E068	-46415
chr15	88578742	88579073	E068	-46023
chr15	88579396	88580245	E068	-44851
chr15	88580713	88580763	E068	-44333
chr15	88581156	88581206	E068	-43890
chr15	88592360	88592457	E068	-32639
chr15	88592917	88592971	E068	-32125
chr15	88593136	88593202	E068	-31894
chr15	88600861	88601006	E068	-24090
chr15	88601173	88601447	E068	-23649
chr15	88602124	88602199	E068	-22897
chr15	88602206	88602632	E068	-22464
chr15	88602642	88602692	E068	-22404
chr15	88602730	88602889	E068	-22207
chr15	88609859	88610435	E068	-14661
chr15	88620449	88620692	E068	-4404
chr15	88620789	88621310	E068	-3786
chr15	88625776	88625940	E068	680
chr15	88625962	88626047	E068	866
chr15	88626078	88626180	E068	982
chr15	88626261	88626311	E068	1165
chr15	88626747	88628062	E068	1651
chr15	88628353	88628424	E068	3257
chr15	88633013	88633169	E068	7917
chr15	88657945	88657999	E068	32849
chr15	88659281	88659417	E068	34185
chr15	88661198	88661253	E068	36102
chr15	88661464	88661553	E068	36368
chr15	88661943	88662095	E068	36847
chr15	88663239	88663306	E068	38143
chr15	88663310	88663360	E068	38214
chr15	88663376	88663566	E068	38280
chr15	88663628	88663811	E068	38532
chr15	88670729	88670967	E068	45633
chr15	88577290	88577339	E069	-47757
chr15	88577645	88577699	E069	-47397
chr15	88579396	88580245	E069	-44851
chr15	88581723	88581773	E069	-43323
chr15	88592360	88592457	E069	-32639
chr15	88592917	88592971	E069	-32125
chr15	88593136	88593202	E069	-31894
chr15	88600861	88601006	E069	-24090
chr15	88601173	88601447	E069	-23649
chr15	88602124	88602199	E069	-22897
chr15	88602206	88602632	E069	-22464
chr15	88602642	88602692	E069	-22404
chr15	88602730	88602889	E069	-22207
chr15	88628353	88628424	E069	3257
chr15	88633203	88634870	E069	8107
chr15	88647965	88648019	E069	22869
chr15	88648423	88648540	E069	23327
chr15	88648645	88648695	E069	23549
chr15	88658447	88659164	E069	33351
chr15	88659281	88659417	E069	34185
chr15	88661198	88661253	E069	36102
chr15	88670729	88670967	E069	45633
chr15	88602124	88602199	E070	-22897
chr15	88602206	88602632	E070	-22464
chr15	88602642	88602692	E070	-22404
chr15	88602730	88602889	E070	-22207
chr15	88663239	88663306	E070	38143
chr15	88663310	88663360	E070	38214
chr15	88663376	88663566	E070	38280
chr15	88663628	88663811	E070	38532
chr15	88577290	88577339	E071	-47757
chr15	88578370	88578681	E071	-46415
chr15	88578742	88579073	E071	-46023
chr15	88579396	88580245	E071	-44851
chr15	88580713	88580763	E071	-44333
chr15	88581156	88581206	E071	-43890
chr15	88592360	88592457	E071	-32639
chr15	88592917	88592971	E071	-32125
chr15	88593136	88593202	E071	-31894
chr15	88600861	88601006	E071	-24090
chr15	88601173	88601447	E071	-23649
chr15	88602124	88602199	E071	-22897
chr15	88602206	88602632	E071	-22464
chr15	88602642	88602692	E071	-22404
chr15	88602730	88602889	E071	-22207
chr15	88612794	88613304	E071	-11792
chr15	88613450	88613500	E071	-11596
chr15	88613957	88614052	E071	-11044
chr15	88626078	88626180	E071	982
chr15	88626747	88628062	E071	1651
chr15	88628353	88628424	E071	3257
chr15	88658447	88659164	E071	33351
chr15	88659281	88659417	E071	34185
chr15	88661198	88661253	E071	36102
chr15	88661464	88661553	E071	36368
chr15	88662987	88663100	E071	37891
chr15	88663239	88663306	E071	38143
chr15	88663310	88663360	E071	38214
chr15	88663376	88663566	E071	38280
chr15	88577645	88577699	E072	-47397
chr15	88577941	88577991	E072	-47105
chr15	88578008	88578099	E072	-46997
chr15	88578110	88578160	E072	-46936
chr15	88578370	88578681	E072	-46415
chr15	88578742	88579073	E072	-46023
chr15	88580713	88580763	E072	-44333
chr15	88592360	88592457	E072	-32639
chr15	88592917	88592971	E072	-32125
chr15	88593136	88593202	E072	-31894
chr15	88601173	88601447	E072	-23649
chr15	88602124	88602199	E072	-22897
chr15	88602206	88602632	E072	-22464
chr15	88612794	88613304	E072	-11792
chr15	88613450	88613500	E072	-11596
chr15	88620449	88620692	E072	-4404
chr15	88620789	88621310	E072	-3786
chr15	88621379	88621433	E072	-3663
chr15	88626747	88628062	E072	1651
chr15	88648645	88648695	E072	23549
chr15	88658447	88659164	E072	33351
chr15	88659281	88659417	E072	34185
chr15	88668877	88669123	E072	43781
chr15	88670051	88670632	E072	44955
chr15	88670729	88670967	E072	45633
chr15	88577645	88577699	E073	-47397
chr15	88577941	88577991	E073	-47105
chr15	88578008	88578099	E073	-46997
chr15	88578110	88578160	E073	-46936
chr15	88578370	88578681	E073	-46415
chr15	88578742	88579073	E073	-46023
chr15	88579396	88580245	E073	-44851
chr15	88592360	88592457	E073	-32639
chr15	88592917	88592971	E073	-32125
chr15	88593136	88593202	E073	-31894
chr15	88602124	88602199	E073	-22897
chr15	88602206	88602632	E073	-22464
chr15	88602642	88602692	E073	-22404
chr15	88602730	88602889	E073	-22207
chr15	88603895	88603950	E073	-21146
chr15	88604669	88604987	E073	-20109
chr15	88610465	88610545	E073	-14551
chr15	88612794	88613304	E073	-11792
chr15	88620449	88620692	E073	-4404
chr15	88620789	88621310	E073	-3786
chr15	88626261	88626311	E073	1165
chr15	88626747	88628062	E073	1651
chr15	88628353	88628424	E073	3257
chr15	88628611	88628661	E073	3515
chr15	88628682	88628723	E073	3586
chr15	88628797	88628874	E073	3701
chr15	88628970	88629010	E073	3874
chr15	88632296	88632560	E073	7200
chr15	88632577	88632927	E073	7481
chr15	88633013	88633169	E073	7917
chr15	88649401	88649686	E073	24305
chr15	88649724	88649870	E073	24628
chr15	88658447	88659164	E073	33351
chr15	88661198	88661253	E073	36102
chr15	88661464	88661553	E073	36368
chr15	88661943	88662095	E073	36847
chr15	88662543	88662593	E073	37447
chr15	88662987	88663100	E073	37891
chr15	88667502	88667759	E073	42406
chr15	88668018	88668109	E073	42922
chr15	88670051	88670632	E073	44955
chr15	88670729	88670967	E073	45633
chr15	88671149	88671252	E073	46053
chr15	88671384	88671434	E073	46288
chr15	88577645	88577699	E074	-47397
chr15	88577941	88577991	E074	-47105
chr15	88578008	88578099	E074	-46997
chr15	88578110	88578160	E074	-46936
chr15	88578370	88578681	E074	-46415
chr15	88578742	88579073	E074	-46023
chr15	88579396	88580245	E074	-44851
chr15	88580713	88580763	E074	-44333
chr15	88581156	88581206	E074	-43890
chr15	88581435	88581495	E074	-43601
chr15	88581723	88581773	E074	-43323
chr15	88592360	88592457	E074	-32639
chr15	88592917	88592971	E074	-32125
chr15	88593136	88593202	E074	-31894
chr15	88600861	88601006	E074	-24090
chr15	88601173	88601447	E074	-23649
chr15	88602124	88602199	E074	-22897
chr15	88602730	88602889	E074	-22207
chr15	88604669	88604987	E074	-20109
chr15	88628353	88628424	E074	3257
chr15	88647669	88647944	E074	22573
chr15	88647965	88648019	E074	22869
chr15	88649401	88649686	E074	24305
chr15	88649724	88649870	E074	24628
chr15	88663239	88663306	E074	38143
chr15	88663310	88663360	E074	38214
chr15	88663376	88663566	E074	38280
chr15	88667502	88667759	E074	42406
chr15	88670729	88670967	E074	45633
chr15	88671149	88671252	E074	46053
chr15	88578742	88579073	E081	-46023
chr15	88579396	88580245	E081	-44851
chr15	88600418	88600482	E081	-24614
chr15	88600791	88600860	E081	-24236
chr15	88600861	88601006	E081	-24090
chr15	88601173	88601447	E081	-23649
chr15	88602124	88602199	E081	-22897
chr15	88602206	88602632	E081	-22464
chr15	88602642	88602692	E081	-22404
chr15	88602730	88602889	E081	-22207
chr15	88611790	88611912	E081	-13184
chr15	88612519	88612573	E081	-12523
chr15	88612794	88613304	E081	-11792
chr15	88613450	88613500	E081	-11596
chr15	88613957	88614052	E081	-11044
chr15	88624281	88624474	E081	-622
chr15	88624569	88624619	E081	-477
chr15	88626747	88628062	E081	1651
chr15	88628353	88628424	E081	3257
chr15	88633203	88634870	E081	8107
chr15	88641652	88642077	E081	16556
chr15	88642476	88642530	E081	17380
chr15	88642538	88642633	E081	17442
chr15	88642771	88642811	E081	17675
chr15	88642889	88642929	E081	17793
chr15	88643031	88643095	E081	17935
chr15	88643350	88643824	E081	18254
chr15	88651289	88651339	E081	26193
chr15	88651690	88652142	E081	26594
chr15	88652188	88652265	E081	27092
chr15	88652374	88652424	E081	27278
chr15	88658447	88659164	E081	33351
chr15	88663239	88663306	E081	38143
chr15	88663310	88663360	E081	38214
chr15	88663376	88663566	E081	38280
chr15	88663628	88663811	E081	38532
chr15	88665106	88665625	E081	40010
chr15	88578370	88578681	E082	-46415
chr15	88578742	88579073	E082	-46023
chr15	88600861	88601006	E082	-24090
chr15	88601173	88601447	E082	-23649
chr15	88602124	88602199	E082	-22897
chr15	88602206	88602632	E082	-22464
chr15	88612794	88613304	E082	-11792
chr15	88613450	88613500	E082	-11596
chr15	88613957	88614052	E082	-11044
chr15	88626747	88628062	E082	1651
chr15	88628353	88628424	E082	3257
chr15	88628611	88628661	E082	3515
chr15	88628682	88628723	E082	3586
chr15	88628797	88628874	E082	3701
chr15	88628970	88629010	E082	3874
chr15	88636903	88636953	E082	11807
chr15	88641032	88641269	E082	15936
chr15	88642771	88642811	E082	17675
chr15	88642889	88642929	E082	17793
chr15	88643031	88643095	E082	17935
chr15	88643350	88643824	E082	18254
chr15	88649401	88649686	E082	24305
chr15	88649724	88649870	E082	24628
chr15	88651289	88651339	E082	26193
chr15	88651690	88652142	E082	26594
chr15	88652188	88652265	E082	27092
chr15	88652374	88652424	E082	27278
chr15	88658447	88659164	E082	33351
chr15	88659281	88659417	E082	34185
chr15	88662987	88663100	E082	37891
chr15	88663239	88663306	E082	38143
chr15	88663310	88663360	E082	38214
chr15	88663376	88663566	E082	38280
chr15	88663628	88663811	E082	38532
chr15	88664272	88664316	E082	39176
chr15	88665106	88665625	E082	40010