rs1569499

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SYNGR1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0376 (11261/29898,GnomAD)
T==0399 (11644/29114,TOPMED)
T==0261 (1307/5008,1000G)
T==0355 (1370/3854,ALSPAC)
T==0335 (1242/3708,TWINSUK)

Position: chr22:39373813 (GRCh38.p7) (22q13.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 347 Enhancers around

Promoter: 36 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.39373813T>C
GRCh37.p13 chr 22	NC_000022.10:g.39769818T>C

Gene: SYNGR1, synaptogyrin 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SYNGR1 transcript variant 1a	NM_004711.4:c.	N/A	Intron Variant
SYNGR1 transcript variant 1b	NM_145731.3:c.	N/A	Intron Variant
SYNGR1 transcript variant 1c	NM_145738.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.477	C=0.523
1000Genomes	American	Sub	694	T=0.250	C=0.750
1000Genomes	East Asian	Sub	1008	T=0.015	C=0.985
1000Genomes	Europe	Sub	1006	T=0.374	C=0.626
1000Genomes	Global	Study-wide	5008	T=0.261	C=0.739
1000Genomes	South Asian	Sub	978	T=0.120	C=0.880
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.355	C=0.645
The Genome Aggregation Database	African	Sub	8702	T=0.463	C=0.537
The Genome Aggregation Database	American	Sub	834	T=0.230	C=0.770
The Genome Aggregation Database	East Asian	Sub	1620	T=0.010	C=0.990
The Genome Aggregation Database	Europe	Sub	18442	T=0.375	C=0.624
The Genome Aggregation Database	Global	Study-wide	29898	T=0.376	C=0.623
The Genome Aggregation Database	Other	Sub	300	T=0.330	C=0.670
Trans-Omics for Precision Medicine	Global	Study-wide	29114	T=0.399	C=0.600
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.335	C=0.665

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
rs1569499	0.0000554	alcoholism	pha002891
rs1569499	0.0000554	alcohol dependence	20201924

eQTL of rs1569499 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr22:39769818	SYNGR1	ENSG00000100321.10	T>C	3.4749e-3	23888	Cerebellum
Chr22:39769818	TAB1	ENSG00000100324.9	T>C	8.3425e-5	-25928	Cerebellum
Chr22:39769818	TAB1	ENSG00000100324.9	T>C	1.2610e-3	-25928	Cerebellar_Hemisphere
Chr22:39769818	TAB1	ENSG00000100324.9	T>C	5.9229e-5	-25928	Brain_Spinal_cord_cervical

meQTL of rs1569499 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 )
chr22	39740125	39740317	E067	-29501
chr22	39747253	39748836	E067	-20982
chr22	39749418	39749798	E067	-20020
chr22	39756071	39756219	E067	-13599
chr22	39759478	39759528	E067	-10290
chr22	39759585	39759639	E067	-10179
chr22	39759655	39759705	E067	-10113
chr22	39759749	39759819	E067	-9999
chr22	39759825	39760379	E067	-9439
chr22	39760450	39760523	E067	-9295
chr22	39760555	39760639	E067	-9179
chr22	39760725	39761343	E067	-8475
chr22	39761374	39761687	E067	-8131
chr22	39761745	39761795	E067	-8023
chr22	39796942	39797016	E067	27124
chr22	39797125	39797194	E067	27307
chr22	39797280	39797320	E067	27462
chr22	39797364	39797418	E067	27546
chr22	39797453	39797503	E067	27635
chr22	39797678	39797734	E067	27860
chr22	39800834	39800978	E067	31016
chr22	39805443	39805507	E067	35625
chr22	39805672	39805773	E067	35854
chr22	39807913	39807993	E067	38095
chr22	39808079	39808159	E067	38261
chr22	39810454	39810622	E067	40636
chr22	39810641	39810702	E067	40823
chr22	39810869	39811312	E067	41051
chr22	39811314	39811374	E067	41496
chr22	39811477	39811531	E067	41659
chr22	39728515	39729151	E068	-40667
chr22	39739329	39739409	E068	-30409
chr22	39739454	39740121	E068	-29697
chr22	39744763	39744848	E068	-24970
chr22	39747253	39748836	E068	-20982
chr22	39758753	39758803	E068	-11015
chr22	39758887	39758967	E068	-10851
chr22	39759014	39759172	E068	-10646
chr22	39759478	39759528	E068	-10290
chr22	39759585	39759639	E068	-10179
chr22	39759655	39759705	E068	-10113
chr22	39759749	39759819	E068	-9999
chr22	39759825	39760379	E068	-9439
chr22	39760450	39760523	E068	-9295
chr22	39760555	39760639	E068	-9179
chr22	39760725	39761343	E068	-8475
chr22	39796942	39797016	E068	27124
chr22	39797125	39797194	E068	27307
chr22	39797280	39797320	E068	27462
chr22	39797364	39797418	E068	27546
chr22	39797453	39797503	E068	27635
chr22	39797678	39797734	E068	27860
chr22	39800834	39800978	E068	31016
chr22	39805443	39805507	E068	35625
chr22	39805672	39805773	E068	35854
chr22	39809797	39809847	E068	39979
chr22	39809936	39810006	E068	40118
chr22	39810285	39810368	E068	40467
chr22	39810454	39810622	E068	40636
chr22	39810641	39810702	E068	40823
chr22	39810869	39811312	E068	41051
chr22	39811314	39811374	E068	41496
chr22	39812365	39812570	E068	42547
chr22	39812572	39812679	E068	42754
chr22	39812786	39812905	E068	42968
chr22	39812991	39813045	E068	43173
chr22	39728515	39729151	E069	-40667
chr22	39739329	39739409	E069	-30409
chr22	39739454	39740121	E069	-29697
chr22	39744763	39744848	E069	-24970
chr22	39758753	39758803	E069	-11015
chr22	39758887	39758967	E069	-10851
chr22	39759014	39759172	E069	-10646
chr22	39759478	39759528	E069	-10290
chr22	39759585	39759639	E069	-10179
chr22	39759655	39759705	E069	-10113
chr22	39759749	39759819	E069	-9999
chr22	39759825	39760379	E069	-9439
chr22	39760450	39760523	E069	-9295
chr22	39760555	39760639	E069	-9179
chr22	39796942	39797016	E069	27124
chr22	39797125	39797194	E069	27307
chr22	39797280	39797320	E069	27462
chr22	39797364	39797418	E069	27546
chr22	39797453	39797503	E069	27635
chr22	39797678	39797734	E069	27860
chr22	39800834	39800978	E069	31016
chr22	39805224	39805264	E069	35406
chr22	39805443	39805507	E069	35625
chr22	39805672	39805773	E069	35854
chr22	39806067	39806150	E069	36249
chr22	39806436	39806603	E069	36618
chr22	39809936	39810006	E069	40118
chr22	39810285	39810368	E069	40467
chr22	39810454	39810622	E069	40636
chr22	39810641	39810702	E069	40823
chr22	39810869	39811312	E069	41051
chr22	39811314	39811374	E069	41496
chr22	39811477	39811531	E069	41659
chr22	39811588	39811638	E069	41770
chr22	39728515	39729151	E070	-40667
chr22	39744594	39744644	E070	-25174
chr22	39744763	39744848	E070	-24970
chr22	39759478	39759528	E070	-10290
chr22	39759585	39759639	E070	-10179
chr22	39759655	39759705	E070	-10113
chr22	39797125	39797194	E070	27307
chr22	39797280	39797320	E070	27462
chr22	39797364	39797418	E070	27546
chr22	39797453	39797503	E070	27635
chr22	39797678	39797734	E070	27860
chr22	39797892	39797966	E070	28074
chr22	39798117	39798172	E070	28299
chr22	39798975	39799023	E070	29157
chr22	39799034	39799078	E070	29216
chr22	39799180	39799264	E070	29362
chr22	39799305	39799355	E070	29487
chr22	39799520	39799587	E070	29702
chr22	39728044	39728226	E071	-41592
chr22	39739454	39740121	E071	-29697
chr22	39744594	39744644	E071	-25174
chr22	39744763	39744848	E071	-24970
chr22	39747253	39748836	E071	-20982
chr22	39749418	39749798	E071	-20020
chr22	39752528	39752755	E071	-17063
chr22	39758115	39758720	E071	-11098
chr22	39758753	39758803	E071	-11015
chr22	39758887	39758967	E071	-10851
chr22	39759014	39759172	E071	-10646
chr22	39759478	39759528	E071	-10290
chr22	39759585	39759639	E071	-10179
chr22	39759655	39759705	E071	-10113
chr22	39759749	39759819	E071	-9999
chr22	39759825	39760379	E071	-9439
chr22	39760450	39760523	E071	-9295
chr22	39760555	39760639	E071	-9179
chr22	39760725	39761343	E071	-8475
chr22	39761374	39761687	E071	-8131
chr22	39761745	39761795	E071	-8023
chr22	39764032	39764205	E071	-5613
chr22	39764221	39764274	E071	-5544
chr22	39764360	39764425	E071	-5393
chr22	39796942	39797016	E071	27124
chr22	39797125	39797194	E071	27307
chr22	39797364	39797418	E071	27546
chr22	39797453	39797503	E071	27635
chr22	39797678	39797734	E071	27860
chr22	39802503	39802558	E071	32685
chr22	39803032	39803116	E071	33214
chr22	39803204	39803265	E071	33386
chr22	39803738	39803788	E071	33920
chr22	39803903	39804100	E071	34085
chr22	39804245	39804490	E071	34427
chr22	39804827	39804884	E071	35009
chr22	39804919	39804972	E071	35101
chr22	39805224	39805264	E071	35406
chr22	39805672	39805773	E071	35854
chr22	39806067	39806150	E071	36249
chr22	39806436	39806603	E071	36618
chr22	39807585	39807671	E071	37767
chr22	39807913	39807993	E071	38095
chr22	39808079	39808159	E071	38261
chr22	39808318	39808963	E071	38500
chr22	39809797	39809847	E071	39979
chr22	39809936	39810006	E071	40118
chr22	39810285	39810368	E071	40467
chr22	39810454	39810622	E071	40636
chr22	39810641	39810702	E071	40823
chr22	39810869	39811312	E071	41051
chr22	39811314	39811374	E071	41496
chr22	39811477	39811531	E071	41659
chr22	39811588	39811638	E071	41770
chr22	39811970	39812014	E071	42152
chr22	39728515	39729151	E072	-40667
chr22	39744763	39744848	E072	-24970
chr22	39755846	39756065	E072	-13753
chr22	39758753	39758803	E072	-11015
chr22	39758887	39758967	E072	-10851
chr22	39759014	39759172	E072	-10646
chr22	39759478	39759528	E072	-10290
chr22	39759585	39759639	E072	-10179
chr22	39759655	39759705	E072	-10113
chr22	39759749	39759819	E072	-9999
chr22	39759825	39760379	E072	-9439
chr22	39760450	39760523	E072	-9295
chr22	39760555	39760639	E072	-9179
chr22	39760725	39761343	E072	-8475
chr22	39805443	39805507	E072	35625
chr22	39805672	39805773	E072	35854
chr22	39806067	39806150	E072	36249
chr22	39806436	39806603	E072	36618
chr22	39807585	39807671	E072	37767
chr22	39807913	39807993	E072	38095
chr22	39808079	39808159	E072	38261
chr22	39809936	39810006	E072	40118
chr22	39810285	39810368	E072	40467
chr22	39810454	39810622	E072	40636
chr22	39810641	39810702	E072	40823
chr22	39810869	39811312	E072	41051
chr22	39811314	39811374	E072	41496
chr22	39739329	39739409	E073	-30409
chr22	39739454	39740121	E073	-29697
chr22	39752528	39752755	E073	-17063
chr22	39752784	39752900	E073	-16918
chr22	39755032	39755076	E073	-14742
chr22	39755279	39755329	E073	-14489
chr22	39755680	39755757	E073	-14061
chr22	39755846	39756065	E073	-13753
chr22	39756071	39756219	E073	-13599
chr22	39756393	39756527	E073	-13291
chr22	39756695	39756820	E073	-12998
chr22	39756898	39757465	E073	-12353
chr22	39757679	39757735	E073	-12083
chr22	39757799	39757905	E073	-11913
chr22	39757992	39758042	E073	-11776
chr22	39758115	39758720	E073	-11098
chr22	39758753	39758803	E073	-11015
chr22	39758887	39758967	E073	-10851
chr22	39759014	39759172	E073	-10646
chr22	39759478	39759528	E073	-10290
chr22	39759585	39759639	E073	-10179
chr22	39759655	39759705	E073	-10113
chr22	39759749	39759819	E073	-9999
chr22	39759825	39760379	E073	-9439
chr22	39760450	39760523	E073	-9295
chr22	39760555	39760639	E073	-9179
chr22	39760725	39761343	E073	-8475
chr22	39761374	39761687	E073	-8131
chr22	39761745	39761795	E073	-8023
chr22	39764032	39764205	E073	-5613
chr22	39764221	39764274	E073	-5544
chr22	39764360	39764425	E073	-5393
chr22	39764479	39765083	E073	-4735
chr22	39765153	39765234	E073	-4584
chr22	39765391	39765526	E073	-4292
chr22	39796942	39797016	E073	27124
chr22	39797125	39797194	E073	27307
chr22	39797280	39797320	E073	27462
chr22	39797364	39797418	E073	27546
chr22	39797453	39797503	E073	27635
chr22	39797678	39797734	E073	27860
chr22	39797892	39797966	E073	28074
chr22	39800834	39800978	E073	31016
chr22	39805443	39805507	E073	35625
chr22	39809936	39810006	E073	40118
chr22	39810285	39810368	E073	40467
chr22	39810454	39810622	E073	40636
chr22	39810641	39810702	E073	40823
chr22	39728515	39729151	E074	-40667
chr22	39739329	39739409	E074	-30409
chr22	39739454	39740121	E074	-29697
chr22	39796942	39797016	E074	27124
chr22	39797125	39797194	E074	27307
chr22	39797280	39797320	E074	27462
chr22	39797364	39797418	E074	27546
chr22	39797453	39797503	E074	27635
chr22	39797678	39797734	E074	27860
chr22	39797892	39797966	E074	28074
chr22	39800834	39800978	E074	31016
chr22	39801024	39801157	E074	31206
chr22	39803903	39804100	E074	34085
chr22	39804245	39804490	E074	34427
chr22	39804827	39804884	E074	35009
chr22	39804919	39804972	E074	35101
chr22	39805224	39805264	E074	35406
chr22	39805443	39805507	E074	35625
chr22	39805672	39805773	E074	35854
chr22	39806067	39806150	E074	36249
chr22	39806436	39806603	E074	36618
chr22	39807585	39807671	E074	37767
chr22	39807913	39807993	E074	38095
chr22	39810285	39810368	E074	40467
chr22	39810454	39810622	E074	40636
chr22	39810641	39810702	E074	40823
chr22	39810869	39811312	E074	41051
chr22	39811314	39811374	E074	41496
chr22	39811477	39811531	E074	41659
chr22	39811588	39811638	E074	41770
chr22	39811970	39812014	E074	42152
chr22	39812240	39812280	E074	42422
chr22	39812365	39812570	E074	42547
chr22	39812572	39812679	E074	42754
chr22	39744763	39744848	E081	-24970
chr22	39747253	39748836	E081	-20982
chr22	39749418	39749798	E081	-20020
chr22	39751905	39751986	E081	-17832
chr22	39752528	39752755	E081	-17063
chr22	39752784	39752900	E081	-16918
chr22	39752903	39753067	E081	-16751
chr22	39753209	39753336	E081	-16482
chr22	39753378	39753424	E081	-16394
chr22	39758115	39758720	E081	-11098
chr22	39758753	39758803	E081	-11015
chr22	39758887	39758967	E081	-10851
chr22	39759014	39759172	E081	-10646
chr22	39759478	39759528	E081	-10290
chr22	39759585	39759639	E081	-10179
chr22	39759655	39759705	E081	-10113
chr22	39759749	39759819	E081	-9999
chr22	39759825	39760379	E081	-9439
chr22	39760450	39760523	E081	-9295
chr22	39760555	39760639	E081	-9179
chr22	39760725	39761343	E081	-8475
chr22	39761374	39761687	E081	-8131
chr22	39761745	39761795	E081	-8023
chr22	39791863	39791956	E081	22045
chr22	39791964	39792018	E081	22146
chr22	39792054	39792275	E081	22236
chr22	39792341	39792438	E081	22523
chr22	39792551	39792655	E081	22733
chr22	39792684	39792740	E081	22866
chr22	39793004	39793202	E081	23186
chr22	39793716	39793770	E081	23898
chr22	39793854	39793904	E081	24036
chr22	39794369	39794410	E081	24551
chr22	39796942	39797016	E081	27124
chr22	39797125	39797194	E081	27307
chr22	39800834	39800978	E081	31016
chr22	39801024	39801157	E081	31206
chr22	39752784	39752900	E082	-16918
chr22	39752903	39753067	E082	-16751
chr22	39753209	39753336	E082	-16482
chr22	39753378	39753424	E082	-16394
chr22	39755846	39756065	E082	-13753
chr22	39756071	39756219	E082	-13599
chr22	39757992	39758042	E082	-11776
chr22	39758115	39758720	E082	-11098
chr22	39758753	39758803	E082	-11015
chr22	39758887	39758967	E082	-10851
chr22	39759014	39759172	E082	-10646
chr22	39759478	39759528	E082	-10290
chr22	39759585	39759639	E082	-10179
chr22	39759655	39759705	E082	-10113
chr22	39759749	39759819	E082	-9999
chr22	39759825	39760379	E082	-9439
chr22	39760450	39760523	E082	-9295
chr22	39760555	39760639	E082	-9179
chr22	39760725	39761343	E082	-8475
chr22	39761374	39761687	E082	-8131
chr22	39761745	39761795	E082	-8023
chr22	39764032	39764205	E082	-5613
chr22	39764221	39764274	E082	-5544
chr22	39764360	39764425	E082	-5393
chr22	39792054	39792275	E082	22236
chr22	39792341	39792438	E082	22523
chr22	39792551	39792655	E082	22733
chr22	39792684	39792740	E082	22866

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	39744862	39747068	E067	-22750
chr22	39784188	39785180	E067	14370
chr22	39795185	39795304	E067	25367
chr22	39795316	39796720	E067	25498
chr22	39744862	39747068	E068	-22750
chr22	39784188	39785180	E068	14370
chr22	39795185	39795304	E068	25367
chr22	39795316	39796720	E068	25498
chr22	39744862	39747068	E069	-22750
chr22	39784188	39785180	E069	14370
chr22	39795185	39795304	E069	25367
chr22	39795316	39796720	E069	25498
chr22	39744862	39747068	E070	-22750
chr22	39795316	39796720	E070	25498
chr22	39744862	39747068	E071	-22750
chr22	39784188	39785180	E071	14370
chr22	39795185	39795304	E071	25367
chr22	39795316	39796720	E071	25498
chr22	39744862	39747068	E072	-22750
chr22	39784188	39785180	E072	14370
chr22	39795185	39795304	E072	25367
chr22	39795316	39796720	E072	25498
chr22	39744862	39747068	E073	-22750
chr22	39784188	39785180	E073	14370
chr22	39795185	39795304	E073	25367
chr22	39795316	39796720	E073	25498
chr22	39744862	39747068	E074	-22750
chr22	39784188	39785180	E074	14370
chr22	39795185	39795304	E074	25367
chr22	39795316	39796720	E074	25498
chr22	39744862	39747068	E081	-22750
chr22	39795185	39795304	E081	25367
chr22	39795316	39796720	E081	25498
chr22	39744862	39747068	E082	-22750
chr22	39795185	39795304	E082	25367
chr22	39795316	39796720	E082	25498