rs4877900

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

NTRK2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0466 (13962/29920,GnomAD)
C==0455 (13266/29118,TOPMED)
C==0487 (2441/5008,1000G)
C==0434 (1674/3854,ALSPAC)
C==0428 (1586/3708,TWINSUK)

Position: chr9:85017403 (GRCh38.p7) (9q21.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 401 Enhancers around

Promoter: 3 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.85017403C>T
GRCh37.p13 chr 9	NC_000009.11:g.87632318C>T
NTRK2 RefSeqGene	NG_012201.2:g.353853C>T

Gene: NTRK2, neurotrophic receptor tyrosine kinase 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NTRK2 transcript variant c	NM_001018064.2:c.	N/A	Intron Variant
NTRK2 transcript variant a	NM_006180.4:c.	N/A	Intron Variant
NTRK2 transcript variant b	NM_001007097.2:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant d	NM_001018065.2:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant e	NM_001018066.2:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant f	NM_001291937.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X1	XM_005252001.2:c.	N/A	Intron Variant
NTRK2 transcript variant X2	XM_005252003.2:c.	N/A	Intron Variant
NTRK2 transcript variant X3	XM_005252004.2:c.	N/A	Intron Variant
NTRK2 transcript variant X5	XM_011518718.2:c.	N/A	Intron Variant
NTRK2 transcript variant X3	XM_017014751.1:c.	N/A	Intron Variant
NTRK2 transcript variant X6	XM_017014752.1:c.	N/A	Intron Variant
NTRK2 transcript variant X7	XM_017014753.1:c.	N/A	Intron Variant
NTRK2 transcript variant X8	XM_017014754.1:c.	N/A	Intron Variant
NTRK2 transcript variant X9	XM_005252006.3:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X14	XM_005252007.3:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X12	XM_011518720.2:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X10	XM_017014755.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X11	XM_017014756.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X13	XM_017014757.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X15	XM_017014758.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X16	XM_017014759.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X17	XM_017014760.1:c.	N/A	Genic Downstream Transcript Variant
NTRK2 transcript variant X18	XM_017014761.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.437	T=0.563
1000Genomes	American	Sub	694	C=0.510	T=0.490
1000Genomes	East Asian	Sub	1008	C=0.683	T=0.317
1000Genomes	Europe	Sub	1006	C=0.435	T=0.565
1000Genomes	Global	Study-wide	5008	C=0.487	T=0.513
1000Genomes	South Asian	Sub	978	C=0.390	T=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.434	T=0.566
The Genome Aggregation Database	African	Sub	8702	C=0.450	T=0.550
The Genome Aggregation Database	American	Sub	838	C=0.550	T=0.450
The Genome Aggregation Database	East Asian	Sub	1612	C=0.638	T=0.362
The Genome Aggregation Database	Europe	Sub	18466	C=0.455	T=0.544
The Genome Aggregation Database	Global	Study-wide	29920	C=0.466	T=0.533
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.455	T=0.544
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.428	T=0.572

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4877900	0.000906	alcohol dependence	21314694

eQTL of rs4877900 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 rs4877900 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 )
chr9	87600550	87600604	E067	-31714
chr9	87603112	87603182	E067	-29136
chr9	87603186	87603306	E067	-29012
chr9	87603660	87603710	E067	-28608
chr9	87603715	87604011	E067	-28307
chr9	87604610	87604683	E067	-27635
chr9	87604934	87606078	E067	-26240
chr9	87606548	87606721	E067	-25597
chr9	87607456	87607590	E067	-24728
chr9	87607961	87608434	E067	-23884
chr9	87608470	87608522	E067	-23796
chr9	87609363	87609407	E067	-22911
chr9	87609476	87609625	E067	-22693
chr9	87609699	87609879	E067	-22439
chr9	87610081	87610508	E067	-21810
chr9	87610666	87610716	E067	-21602
chr9	87610804	87611538	E067	-20780
chr9	87612442	87612663	E067	-19655
chr9	87612715	87612799	E067	-19519
chr9	87612848	87612931	E067	-19387
chr9	87620594	87620634	E067	-11684
chr9	87624257	87624318	E067	-8000
chr9	87624346	87624409	E067	-7909
chr9	87630411	87630550	E067	-1768
chr9	87630586	87630626	E067	-1692
chr9	87631115	87631289	E067	-1029
chr9	87631345	87631771	E067	-547
chr9	87631774	87632088	E067	-230
chr9	87633344	87633398	E067	1026
chr9	87633554	87633742	E067	1236
chr9	87633946	87634006	E067	1628
chr9	87637322	87637372	E067	5004
chr9	87637640	87637736	E067	5322
chr9	87637784	87637854	E067	5466
chr9	87637879	87637929	E067	5561
chr9	87639210	87639270	E067	6892
chr9	87639291	87639403	E067	6973
chr9	87639436	87639546	E067	7118
chr9	87639561	87639642	E067	7243
chr9	87640245	87640335	E067	7927
chr9	87653020	87653354	E067	20702
chr9	87653495	87653552	E067	21177
chr9	87653695	87653752	E067	21377
chr9	87653896	87654043	E067	21578
chr9	87654111	87654178	E067	21793
chr9	87654205	87654389	E067	21887
chr9	87654499	87654623	E067	22181
chr9	87654644	87654723	E067	22326
chr9	87654784	87654824	E067	22466
chr9	87656427	87656597	E067	24109
chr9	87657935	87658291	E067	25617
chr9	87658304	87658427	E067	25986
chr9	87658449	87658595	E067	26131
chr9	87658685	87658735	E067	26367
chr9	87585933	87586050	E068	-46268
chr9	87586281	87586331	E068	-45987
chr9	87589786	87590069	E068	-42249
chr9	87590132	87590264	E068	-42054
chr9	87600550	87600604	E068	-31714
chr9	87603112	87603182	E068	-29136
chr9	87603186	87603306	E068	-29012
chr9	87603660	87603710	E068	-28608
chr9	87603715	87604011	E068	-28307
chr9	87604610	87604683	E068	-27635
chr9	87604934	87606078	E068	-26240
chr9	87607456	87607590	E068	-24728
chr9	87610081	87610508	E068	-21810
chr9	87610666	87610716	E068	-21602
chr9	87610804	87611538	E068	-20780
chr9	87612442	87612663	E068	-19655
chr9	87612715	87612799	E068	-19519
chr9	87612848	87612931	E068	-19387
chr9	87613457	87613547	E068	-18771
chr9	87630411	87630550	E068	-1768
chr9	87630586	87630626	E068	-1692
chr9	87631115	87631289	E068	-1029
chr9	87631345	87631771	E068	-547
chr9	87631774	87632088	E068	-230
chr9	87633344	87633398	E068	1026
chr9	87633554	87633742	E068	1236
chr9	87637322	87637372	E068	5004
chr9	87637640	87637736	E068	5322
chr9	87637784	87637854	E068	5466
chr9	87639210	87639270	E068	6892
chr9	87639291	87639403	E068	6973
chr9	87639436	87639546	E068	7118
chr9	87639561	87639642	E068	7243
chr9	87640245	87640335	E068	7927
chr9	87643369	87643419	E068	11051
chr9	87643719	87643769	E068	11401
chr9	87651216	87651934	E068	18898
chr9	87653495	87653552	E068	21177
chr9	87653695	87653752	E068	21377
chr9	87656427	87656597	E068	24109
chr9	87656779	87656929	E068	24461
chr9	87657351	87657475	E068	25033
chr9	87657730	87657858	E068	25412
chr9	87657935	87658291	E068	25617
chr9	87658304	87658427	E068	25986
chr9	87658449	87658595	E068	26131
chr9	87658685	87658735	E068	26367
chr9	87585421	87585678	E069	-46640
chr9	87586462	87586729	E069	-45589
chr9	87587093	87587338	E069	-44980
chr9	87587908	87588135	E069	-44183
chr9	87590776	87590826	E069	-41492
chr9	87590959	87591127	E069	-41191
chr9	87594070	87594158	E069	-38160
chr9	87603660	87603710	E069	-28608
chr9	87603715	87604011	E069	-28307
chr9	87604610	87604683	E069	-27635
chr9	87604934	87606078	E069	-26240
chr9	87606217	87606319	E069	-25999
chr9	87606548	87606721	E069	-25597
chr9	87606805	87606855	E069	-25463
chr9	87607456	87607590	E069	-24728
chr9	87607961	87608434	E069	-23884
chr9	87609363	87609407	E069	-22911
chr9	87609476	87609625	E069	-22693
chr9	87609699	87609879	E069	-22439
chr9	87610081	87610508	E069	-21810
chr9	87610666	87610716	E069	-21602
chr9	87610804	87611538	E069	-20780
chr9	87613457	87613547	E069	-18771
chr9	87619843	87619902	E069	-12416
chr9	87619911	87620033	E069	-12285
chr9	87620138	87620198	E069	-12120
chr9	87630411	87630550	E069	-1768
chr9	87630586	87630626	E069	-1692
chr9	87631774	87632088	E069	-230
chr9	87633344	87633398	E069	1026
chr9	87633554	87633742	E069	1236
chr9	87633946	87634006	E069	1628
chr9	87634200	87634350	E069	1882
chr9	87634562	87634868	E069	2244
chr9	87637322	87637372	E069	5004
chr9	87637640	87637736	E069	5322
chr9	87637784	87637854	E069	5466
chr9	87637879	87637929	E069	5561
chr9	87639210	87639270	E069	6892
chr9	87639291	87639403	E069	6973
chr9	87639436	87639546	E069	7118
chr9	87639561	87639642	E069	7243
chr9	87640245	87640335	E069	7927
chr9	87651216	87651934	E069	18898
chr9	87653020	87653354	E069	20702
chr9	87653495	87653552	E069	21177
chr9	87653695	87653752	E069	21377
chr9	87653896	87654043	E069	21578
chr9	87654111	87654178	E069	21793
chr9	87654205	87654389	E069	21887
chr9	87654499	87654623	E069	22181
chr9	87654644	87654723	E069	22326
chr9	87654784	87654824	E069	22466
chr9	87656427	87656597	E069	24109
chr9	87656779	87656929	E069	24461
chr9	87657351	87657475	E069	25033
chr9	87657730	87657858	E069	25412
chr9	87657935	87658291	E069	25617
chr9	87658304	87658427	E069	25986
chr9	87658449	87658595	E069	26131
chr9	87590776	87590826	E070	-41492
chr9	87604934	87606078	E070	-26240
chr9	87606217	87606319	E070	-25999
chr9	87606548	87606721	E070	-25597
chr9	87606805	87606855	E070	-25463
chr9	87607456	87607590	E070	-24728
chr9	87607961	87608434	E070	-23884
chr9	87656427	87656597	E070	24109
chr9	87656779	87656929	E070	24461
chr9	87657351	87657475	E070	25033
chr9	87658304	87658427	E070	25986
chr9	87658449	87658595	E070	26131
chr9	87600550	87600604	E071	-31714
chr9	87603660	87603710	E071	-28608
chr9	87603715	87604011	E071	-28307
chr9	87604610	87604683	E071	-27635
chr9	87604934	87606078	E071	-26240
chr9	87606217	87606319	E071	-25999
chr9	87606548	87606721	E071	-25597
chr9	87606805	87606855	E071	-25463
chr9	87607456	87607590	E071	-24728
chr9	87607961	87608434	E071	-23884
chr9	87608470	87608522	E071	-23796
chr9	87609363	87609407	E071	-22911
chr9	87609476	87609625	E071	-22693
chr9	87609699	87609879	E071	-22439
chr9	87610081	87610508	E071	-21810
chr9	87610666	87610716	E071	-21602
chr9	87610804	87611538	E071	-20780
chr9	87612442	87612663	E071	-19655
chr9	87612715	87612799	E071	-19519
chr9	87612848	87612931	E071	-19387
chr9	87613457	87613547	E071	-18771
chr9	87619077	87619160	E071	-13158
chr9	87619843	87619902	E071	-12416
chr9	87619911	87620033	E071	-12285
chr9	87620138	87620198	E071	-12120
chr9	87630411	87630550	E071	-1768
chr9	87630586	87630626	E071	-1692
chr9	87631774	87632088	E071	-230
chr9	87633344	87633398	E071	1026
chr9	87633554	87633742	E071	1236
chr9	87633946	87634006	E071	1628
chr9	87634200	87634350	E071	1882
chr9	87634562	87634868	E071	2244
chr9	87636365	87636445	E071	4047
chr9	87636468	87636560	E071	4150
chr9	87636601	87637179	E071	4283
chr9	87637322	87637372	E071	5004
chr9	87637640	87637736	E071	5322
chr9	87637784	87637854	E071	5466
chr9	87637879	87637929	E071	5561
chr9	87639210	87639270	E071	6892
chr9	87639291	87639403	E071	6973
chr9	87639436	87639546	E071	7118
chr9	87639561	87639642	E071	7243
chr9	87640245	87640335	E071	7927
chr9	87651216	87651934	E071	18898
chr9	87653020	87653354	E071	20702
chr9	87653495	87653552	E071	21177
chr9	87653695	87653752	E071	21377
chr9	87653896	87654043	E071	21578
chr9	87654111	87654178	E071	21793
chr9	87654205	87654389	E071	21887
chr9	87654499	87654623	E071	22181
chr9	87654644	87654723	E071	22326
chr9	87654784	87654824	E071	22466
chr9	87656427	87656597	E071	24109
chr9	87657351	87657475	E071	25033
chr9	87657730	87657858	E071	25412
chr9	87657935	87658291	E071	25617
chr9	87658304	87658427	E071	25986
chr9	87585933	87586050	E072	-46268
chr9	87586281	87586331	E072	-45987
chr9	87586462	87586729	E072	-45589
chr9	87587093	87587338	E072	-44980
chr9	87603112	87603182	E072	-29136
chr9	87603186	87603306	E072	-29012
chr9	87603660	87603710	E072	-28608
chr9	87603715	87604011	E072	-28307
chr9	87604934	87606078	E072	-26240
chr9	87607456	87607590	E072	-24728
chr9	87607961	87608434	E072	-23884
chr9	87610804	87611538	E072	-20780
chr9	87612442	87612663	E072	-19655
chr9	87612715	87612799	E072	-19519
chr9	87612848	87612931	E072	-19387
chr9	87619843	87619902	E072	-12416
chr9	87619911	87620033	E072	-12285
chr9	87620138	87620198	E072	-12120
chr9	87630411	87630550	E072	-1768
chr9	87630586	87630626	E072	-1692
chr9	87631115	87631289	E072	-1029
chr9	87631345	87631771	E072	-547
chr9	87631774	87632088	E072	-230
chr9	87633344	87633398	E072	1026
chr9	87633554	87633742	E072	1236
chr9	87636365	87636445	E072	4047
chr9	87636468	87636560	E072	4150
chr9	87637322	87637372	E072	5004
chr9	87637640	87637736	E072	5322
chr9	87637784	87637854	E072	5466
chr9	87637879	87637929	E072	5561
chr9	87639210	87639270	E072	6892
chr9	87639291	87639403	E072	6973
chr9	87639436	87639546	E072	7118
chr9	87639561	87639642	E072	7243
chr9	87640245	87640335	E072	7927
chr9	87640414	87640480	E072	8096
chr9	87656779	87656929	E072	24461
chr9	87657351	87657475	E072	25033
chr9	87657730	87657858	E072	25412
chr9	87657935	87658291	E072	25617
chr9	87658304	87658427	E072	25986
chr9	87583492	87583614	E073	-48704
chr9	87583954	87584431	E073	-47887
chr9	87585421	87585678	E073	-46640
chr9	87585933	87586050	E073	-46268
chr9	87586281	87586331	E073	-45987
chr9	87586462	87586729	E073	-45589
chr9	87587093	87587338	E073	-44980
chr9	87589786	87590069	E073	-42249
chr9	87590132	87590264	E073	-42054
chr9	87590959	87591127	E073	-41191
chr9	87600550	87600604	E073	-31714
chr9	87603660	87603710	E073	-28608
chr9	87603715	87604011	E073	-28307
chr9	87604610	87604683	E073	-27635
chr9	87604934	87606078	E073	-26240
chr9	87606217	87606319	E073	-25999
chr9	87606805	87606855	E073	-25463
chr9	87607456	87607590	E073	-24728
chr9	87607961	87608434	E073	-23884
chr9	87608470	87608522	E073	-23796
chr9	87609363	87609407	E073	-22911
chr9	87609476	87609625	E073	-22693
chr9	87609699	87609879	E073	-22439
chr9	87610081	87610508	E073	-21810
chr9	87610666	87610716	E073	-21602
chr9	87610804	87611538	E073	-20780
chr9	87612442	87612663	E073	-19655
chr9	87612715	87612799	E073	-19519
chr9	87612848	87612931	E073	-19387
chr9	87613457	87613547	E073	-18771
chr9	87619843	87619902	E073	-12416
chr9	87619911	87620033	E073	-12285
chr9	87620138	87620198	E073	-12120
chr9	87630586	87630626	E073	-1692
chr9	87631115	87631289	E073	-1029
chr9	87631345	87631771	E073	-547
chr9	87636365	87636445	E073	4047
chr9	87636468	87636560	E073	4150
chr9	87639210	87639270	E073	6892
chr9	87639291	87639403	E073	6973
chr9	87639436	87639546	E073	7118
chr9	87639561	87639642	E073	7243
chr9	87640245	87640335	E073	7927
chr9	87653020	87653354	E073	20702
chr9	87653495	87653552	E073	21177
chr9	87653695	87653752	E073	21377
chr9	87653896	87654043	E073	21578
chr9	87654111	87654178	E073	21793
chr9	87654205	87654389	E073	21887
chr9	87654499	87654623	E073	22181
chr9	87656427	87656597	E073	24109
chr9	87656779	87656929	E073	24461
chr9	87657351	87657475	E073	25033
chr9	87657730	87657858	E073	25412
chr9	87657935	87658291	E073	25617
chr9	87658304	87658427	E073	25986
chr9	87586281	87586331	E074	-45987
chr9	87586462	87586729	E074	-45589
chr9	87590776	87590826	E074	-41492
chr9	87590959	87591127	E074	-41191
chr9	87600550	87600604	E074	-31714
chr9	87603660	87603710	E074	-28608
chr9	87603715	87604011	E074	-28307
chr9	87604610	87604683	E074	-27635
chr9	87604934	87606078	E074	-26240
chr9	87606217	87606319	E074	-25999
chr9	87606548	87606721	E074	-25597
chr9	87606805	87606855	E074	-25463
chr9	87607456	87607590	E074	-24728
chr9	87609476	87609625	E074	-22693
chr9	87609699	87609879	E074	-22439
chr9	87610081	87610508	E074	-21810
chr9	87610666	87610716	E074	-21602
chr9	87610804	87611538	E074	-20780
chr9	87612442	87612663	E074	-19655
chr9	87612715	87612799	E074	-19519
chr9	87612848	87612931	E074	-19387
chr9	87620138	87620198	E074	-12120
chr9	87630411	87630550	E074	-1768
chr9	87630586	87630626	E074	-1692
chr9	87631115	87631289	E074	-1029
chr9	87631345	87631771	E074	-547
chr9	87631774	87632088	E074	-230
chr9	87633344	87633398	E074	1026
chr9	87633554	87633742	E074	1236
chr9	87637640	87637736	E074	5322
chr9	87637784	87637854	E074	5466
chr9	87637879	87637929	E074	5561
chr9	87639210	87639270	E074	6892
chr9	87639291	87639403	E074	6973
chr9	87639436	87639546	E074	7118
chr9	87639561	87639642	E074	7243
chr9	87653020	87653354	E074	20702
chr9	87654205	87654389	E074	21887
chr9	87654499	87654623	E074	22181
chr9	87654644	87654723	E074	22326
chr9	87654784	87654824	E074	22466
chr9	87656427	87656597	E074	24109
chr9	87656779	87656929	E074	24461
chr9	87657351	87657475	E074	25033
chr9	87658304	87658427	E074	25986
chr9	87658449	87658595	E074	26131
chr9	87604934	87606078	E081	-26240
chr9	87606217	87606319	E081	-25999
chr9	87606548	87606721	E081	-25597
chr9	87606805	87606855	E081	-25463
chr9	87607456	87607590	E081	-24728
chr9	87610804	87611538	E081	-20780
chr9	87653896	87654043	E081	21578
chr9	87654111	87654178	E081	21793
chr9	87654205	87654389	E081	21887
chr9	87654499	87654623	E081	22181
chr9	87654644	87654723	E081	22326
chr9	87654784	87654824	E081	22466
chr9	87655501	87656284	E081	23183
chr9	87656427	87656597	E081	24109
chr9	87656779	87656929	E081	24461
chr9	87604934	87606078	E082	-26240
chr9	87606217	87606319	E082	-25999
chr9	87606548	87606721	E082	-25597
chr9	87653896	87654043	E082	21578
chr9	87654111	87654178	E082	21793
chr9	87654205	87654389	E082	21887
chr9	87654499	87654623	E082	22181
chr9	87654644	87654723	E082	22326
chr9	87654784	87654824	E082	22466

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	87645090	87645140	E074	12772
chr9	87645208	87645300	E074	12890
chr9	87645312	87645576	E074	12994