rs10413398

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

AP3D1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0309 (9260/29950,GnomAD)
C=0322 (9381/29118,TOPMED)
C=0325 (1628/5008,1000G)
C=0221 (853/3854,ALSPAC)
C=0225 (835/3708,TWINSUK)

Position: chr19:2106697 (GRCh38.p7) (19p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 240 Enhancers around

Promoter: 48 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.2106697T>C
GRCh37.p13 chr 19	NC_000019.9:g.2106696T>C

Gene: AP3D1, adaptor related protein complex 3 delta 1 subunit(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AP3D1 transcript variant 3	NM_001261826.1:c.	N/A	Intron Variant
AP3D1 transcript variant 2	NM_003938.6:c.	N/A	Intron Variant
AP3D1 transcript variant X1	XM_006722932.2:c.	N/A	Intron Variant
AP3D1 transcript variant X2	XM_017027422.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.510	C=0.490
1000Genomes	American	Sub	694	T=0.790	C=0.210
1000Genomes	East Asian	Sub	1008	T=0.670	C=0.330
1000Genomes	Europe	Sub	1006	T=0.803	C=0.197
1000Genomes	Global	Study-wide	5008	T=0.675	C=0.325
1000Genomes	South Asian	Sub	978	T=0.690	C=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.779	C=0.221
The Genome Aggregation Database	African	Sub	8710	T=0.516	C=0.484
The Genome Aggregation Database	American	Sub	836	T=0.780	C=0.220
The Genome Aggregation Database	East Asian	Sub	1616	T=0.616	C=0.384
The Genome Aggregation Database	Europe	Sub	18486	T=0.774	C=0.225
The Genome Aggregation Database	Global	Study-wide	29950	T=0.690	C=0.309
The Genome Aggregation Database	Other	Sub	302	T=0.750	C=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.677	C=0.322
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.775	C=0.225

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
rs10413398	0.000247	alcohol dependence	21314694

eQTL of rs10413398 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 rs10413398 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 )
chr19	2059182	2059233	E067	-47463
chr19	2064431	2064736	E067	-41960
chr19	2064799	2065570	E067	-41126
chr19	2069441	2069629	E067	-37067
chr19	2101226	2101276	E067	-5420
chr19	2101361	2101416	E067	-5280
chr19	2101418	2101508	E067	-5188
chr19	2101590	2101794	E067	-4902
chr19	2101911	2101993	E067	-4703
chr19	2102165	2102267	E067	-4429
chr19	2145189	2145313	E067	38493
chr19	2145430	2145474	E067	38734
chr19	2145581	2145633	E067	38885
chr19	2145643	2145846	E067	38947
chr19	2145857	2146268	E067	39161
chr19	2146285	2146367	E067	39589
chr19	2148297	2148440	E067	41601
chr19	2148477	2148661	E067	41781
chr19	2148680	2148828	E067	41984
chr19	2148886	2149006	E067	42190
chr19	2149089	2149267	E067	42393
chr19	2149565	2149644	E067	42869
chr19	2155974	2156415	E067	49278
chr19	2156421	2156514	E067	49725
chr19	2059087	2059150	E068	-47546
chr19	2059182	2059233	E068	-47463
chr19	2064431	2064736	E068	-41960
chr19	2064799	2065570	E068	-41126
chr19	2089471	2090835	E068	-15861
chr19	2090960	2091010	E068	-15686
chr19	2092356	2092503	E068	-14193
chr19	2092599	2092701	E068	-13995
chr19	2092780	2093187	E068	-13509
chr19	2100795	2100882	E068	-5814
chr19	2100925	2100984	E068	-5712
chr19	2101035	2101108	E068	-5588
chr19	2101226	2101276	E068	-5420
chr19	2101361	2101416	E068	-5280
chr19	2101418	2101508	E068	-5188
chr19	2101590	2101794	E068	-4902
chr19	2138220	2138278	E068	31524
chr19	2138429	2138662	E068	31733
chr19	2145430	2145474	E068	38734
chr19	2145581	2145633	E068	38885
chr19	2145643	2145846	E068	38947
chr19	2145857	2146268	E068	39161
chr19	2146285	2146367	E068	39589
chr19	2148297	2148440	E068	41601
chr19	2148477	2148661	E068	41781
chr19	2149089	2149267	E068	42393
chr19	2149565	2149644	E068	42869
chr19	2065590	2065636	E069	-41060
chr19	2069441	2069629	E069	-37067
chr19	2069662	2070187	E069	-36509
chr19	2088885	2089396	E069	-17300
chr19	2089471	2090835	E069	-15861
chr19	2090960	2091010	E069	-15686
chr19	2093295	2093489	E069	-13207
chr19	2101035	2101108	E069	-5588
chr19	2101226	2101276	E069	-5420
chr19	2101361	2101416	E069	-5280
chr19	2101418	2101508	E069	-5188
chr19	2101590	2101794	E069	-4902
chr19	2127771	2128170	E069	21075
chr19	2128251	2128361	E069	21555
chr19	2144237	2144331	E069	37541
chr19	2144892	2144999	E069	38196
chr19	2145189	2145313	E069	38493
chr19	2145430	2145474	E069	38734
chr19	2145857	2146268	E069	39161
chr19	2146285	2146367	E069	39589
chr19	2146710	2146838	E069	40014
chr19	2146901	2146980	E069	40205
chr19	2148680	2148828	E069	41984
chr19	2148886	2149006	E069	42190
chr19	2149089	2149267	E069	42393
chr19	2149565	2149644	E069	42869
chr19	2155974	2156415	E069	49278
chr19	2156421	2156514	E069	49725
chr19	2058205	2058395	E070	-48301
chr19	2058437	2058771	E070	-47925
chr19	2092780	2093187	E070	-13509
chr19	2093295	2093489	E070	-13207
chr19	2145189	2145313	E070	38493
chr19	2145430	2145474	E070	38734
chr19	2145581	2145633	E070	38885
chr19	2145643	2145846	E070	38947
chr19	2145857	2146268	E070	39161
chr19	2146285	2146367	E070	39589
chr19	2148297	2148440	E070	41601
chr19	2148477	2148661	E070	41781
chr19	2148680	2148828	E070	41984
chr19	2148886	2149006	E070	42190
chr19	2149089	2149267	E070	42393
chr19	2149565	2149644	E070	42869
chr19	2064431	2064736	E071	-41960
chr19	2064799	2065570	E071	-41126
chr19	2069441	2069629	E071	-37067
chr19	2069662	2070187	E071	-36509
chr19	2086989	2088316	E071	-18380
chr19	2088885	2089396	E071	-17300
chr19	2089471	2090835	E071	-15861
chr19	2090960	2091010	E071	-15686
chr19	2091015	2091431	E071	-15265
chr19	2091696	2091746	E071	-14950
chr19	2092356	2092503	E071	-14193
chr19	2092599	2092701	E071	-13995
chr19	2092780	2093187	E071	-13509
chr19	2093295	2093489	E071	-13207
chr19	2100795	2100882	E071	-5814
chr19	2100925	2100984	E071	-5712
chr19	2101035	2101108	E071	-5588
chr19	2101226	2101276	E071	-5420
chr19	2101361	2101416	E071	-5280
chr19	2101418	2101508	E071	-5188
chr19	2101590	2101794	E071	-4902
chr19	2101911	2101993	E071	-4703
chr19	2102165	2102267	E071	-4429
chr19	2137819	2137869	E071	31123
chr19	2137947	2138084	E071	31251
chr19	2138220	2138278	E071	31524
chr19	2138429	2138662	E071	31733
chr19	2145189	2145313	E071	38493
chr19	2145430	2145474	E071	38734
chr19	2145581	2145633	E071	38885
chr19	2145643	2145846	E071	38947
chr19	2145857	2146268	E071	39161
chr19	2146285	2146367	E071	39589
chr19	2146710	2146838	E071	40014
chr19	2146901	2146980	E071	40205
chr19	2148680	2148828	E071	41984
chr19	2148886	2149006	E071	42190
chr19	2149089	2149267	E071	42393
chr19	2149565	2149644	E071	42869
chr19	2155974	2156415	E071	49278
chr19	2156421	2156514	E071	49725
chr19	2064431	2064736	E072	-41960
chr19	2065590	2065636	E072	-41060
chr19	2069441	2069629	E072	-37067
chr19	2069662	2070187	E072	-36509
chr19	2089471	2090835	E072	-15861
chr19	2092599	2092701	E072	-13995
chr19	2101035	2101108	E072	-5588
chr19	2101226	2101276	E072	-5420
chr19	2101361	2101416	E072	-5280
chr19	2101418	2101508	E072	-5188
chr19	2101590	2101794	E072	-4902
chr19	2101911	2101993	E072	-4703
chr19	2102165	2102267	E072	-4429
chr19	2145189	2145313	E072	38493
chr19	2145430	2145474	E072	38734
chr19	2145581	2145633	E072	38885
chr19	2145643	2145846	E072	38947
chr19	2145857	2146268	E072	39161
chr19	2146285	2146367	E072	39589
chr19	2148297	2148440	E072	41601
chr19	2148477	2148661	E072	41781
chr19	2148680	2148828	E072	41984
chr19	2148886	2149006	E072	42190
chr19	2149089	2149267	E072	42393
chr19	2155974	2156415	E072	49278
chr19	2156421	2156514	E072	49725
chr19	2059182	2059233	E073	-47463
chr19	2064431	2064736	E073	-41960
chr19	2064799	2065570	E073	-41126
chr19	2069441	2069629	E073	-37067
chr19	2069662	2070187	E073	-36509
chr19	2089471	2090835	E073	-15861
chr19	2090960	2091010	E073	-15686
chr19	2092599	2092701	E073	-13995
chr19	2092780	2093187	E073	-13509
chr19	2093295	2093489	E073	-13207
chr19	2101035	2101108	E073	-5588
chr19	2101226	2101276	E073	-5420
chr19	2101361	2101416	E073	-5280
chr19	2101418	2101508	E073	-5188
chr19	2101590	2101794	E073	-4902
chr19	2138220	2138278	E073	31524
chr19	2138429	2138662	E073	31733
chr19	2144237	2144331	E073	37541
chr19	2144531	2144571	E073	37835
chr19	2144892	2144999	E073	38196
chr19	2145189	2145313	E073	38493
chr19	2145430	2145474	E073	38734
chr19	2145581	2145633	E073	38885
chr19	2145643	2145846	E073	38947
chr19	2145857	2146268	E073	39161
chr19	2146285	2146367	E073	39589
chr19	2148477	2148661	E073	41781
chr19	2148680	2148828	E073	41984
chr19	2148886	2149006	E073	42190
chr19	2149089	2149267	E073	42393
chr19	2149565	2149644	E073	42869
chr19	2155974	2156415	E073	49278
chr19	2156421	2156514	E073	49725
chr19	2063731	2063801	E074	-42895
chr19	2063814	2063905	E074	-42791
chr19	2063972	2064133	E074	-42563
chr19	2064175	2064215	E074	-42481
chr19	2064431	2064736	E074	-41960
chr19	2089471	2090835	E074	-15861
chr19	2101226	2101276	E074	-5420
chr19	2101361	2101416	E074	-5280
chr19	2101418	2101508	E074	-5188
chr19	2101590	2101794	E074	-4902
chr19	2101911	2101993	E074	-4703
chr19	2145189	2145313	E074	38493
chr19	2145430	2145474	E074	38734
chr19	2145581	2145633	E074	38885
chr19	2145643	2145846	E074	38947
chr19	2145857	2146268	E074	39161
chr19	2146285	2146367	E074	39589
chr19	2146710	2146838	E074	40014
chr19	2146901	2146980	E074	40205
chr19	2148297	2148440	E074	41601
chr19	2148886	2149006	E074	42190
chr19	2149089	2149267	E074	42393
chr19	2149565	2149644	E074	42869
chr19	2064431	2064736	E081	-41960
chr19	2064799	2065570	E081	-41126
chr19	2145581	2145633	E081	38885
chr19	2145643	2145846	E081	38947
chr19	2145857	2146268	E081	39161
chr19	2146901	2146980	E081	40205
chr19	2149089	2149267	E081	42393
chr19	2149565	2149644	E081	42869
chr19	2064799	2065570	E082	-41126
chr19	2145430	2145474	E082	38734
chr19	2145581	2145633	E082	38885
chr19	2145643	2145846	E082	38947
chr19	2145857	2146268	E082	39161
chr19	2146285	2146367	E082	39589
chr19	2146710	2146838	E082	40014
chr19	2146901	2146980	E082	40205
chr19	2148297	2148440	E082	41601
chr19	2148477	2148661	E082	41781
chr19	2148680	2148828	E082	41984
chr19	2148886	2149006	E082	42190
chr19	2149089	2149267	E082	42393
chr19	2149565	2149644	E082	42869

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	2095026	2095193	E067	-11503
chr19	2095205	2095790	E067	-10906
chr19	2095856	2095958	E067	-10738
chr19	2095992	2098875	E067	-7821
chr19	2149869	2152339	E067	43173
chr19	2095026	2095193	E068	-11503
chr19	2095205	2095790	E068	-10906
chr19	2095856	2095958	E068	-10738
chr19	2095992	2098875	E068	-7821
chr19	2149869	2152339	E068	43173
chr19	2095026	2095193	E069	-11503
chr19	2095205	2095790	E069	-10906
chr19	2095856	2095958	E069	-10738
chr19	2095992	2098875	E069	-7821
chr19	2149869	2152339	E069	43173
chr19	2095026	2095193	E070	-11503
chr19	2095205	2095790	E070	-10906
chr19	2095856	2095958	E070	-10738
chr19	2095992	2098875	E070	-7821
chr19	2149869	2152339	E070	43173
chr19	2095026	2095193	E071	-11503
chr19	2095205	2095790	E071	-10906
chr19	2095856	2095958	E071	-10738
chr19	2095992	2098875	E071	-7821
chr19	2149869	2152339	E071	43173
chr19	2095026	2095193	E072	-11503
chr19	2095205	2095790	E072	-10906
chr19	2095856	2095958	E072	-10738
chr19	2095992	2098875	E072	-7821
chr19	2149869	2152339	E072	43173
chr19	2095026	2095193	E073	-11503
chr19	2095205	2095790	E073	-10906
chr19	2095856	2095958	E073	-10738
chr19	2095992	2098875	E073	-7821
chr19	2149869	2152339	E073	43173
chr19	2095026	2095193	E074	-11503
chr19	2095205	2095790	E074	-10906
chr19	2095856	2095958	E074	-10738
chr19	2095992	2098875	E074	-7821
chr19	2149869	2152339	E074	43173
chr19	2095026	2095193	E081	-11503
chr19	2095205	2095790	E081	-10906
chr19	2095856	2095958	E081	-10738
chr19	2095026	2095193	E082	-11503
chr19	2095205	2095790	E082	-10906
chr19	2095856	2095958	E082	-10738
chr19	2095992	2098875	E082	-7821
chr19	2149869	2152339	E082	43173