rs5757642

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SYNGR1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0319 (9570/29932,GnomAD)
T==0313 (9118/29114,TOPMED)
T==0198 (991/5008,1000G)
T==0355 (1368/3854,ALSPAC)
T==0335 (1241/3708,TWINSUK)

Position: chr22:39368819 (GRCh38.p7) (22q13.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 347 Enhancers around

Promoter: 42 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.39368819T>C
GRCh37.p13 chr 22	NC_000022.10:g.39764824T>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=0.256	C=0.744
1000Genomes	American	Sub	694	T=0.230	C=0.770
1000Genomes	East Asian	Sub	1008	T=0.001	C=0.999
1000Genomes	Europe	Sub	1006	T=0.374	C=0.626
1000Genomes	Global	Study-wide	5008	T=0.198	C=0.802
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	8722	T=0.272	C=0.728
The Genome Aggregation Database	American	Sub	838	T=0.220	C=0.780
The Genome Aggregation Database	East Asian	Sub	1622	T=0.001	C=0.999
The Genome Aggregation Database	Europe	Sub	18448	T=0.374	C=0.625
The Genome Aggregation Database	Global	Study-wide	29932	T=0.319	C=0.680
The Genome Aggregation Database	Other	Sub	302	T=0.340	C=0.660
Trans-Omics for Precision Medicine	Global	Study-wide	29114	T=0.313	C=0.686
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
rs5757642	0.0001	alcohol dependence	20201924

eQTL of rs5757642 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr22:39764824	SYNGR1	ENSG00000100321.10	T>C	3.4749e-3	18894	Cerebellum
Chr22:39764824	TAB1	ENSG00000100324.9	T>C	8.3425e-5	-30922	Cerebellum

meQTL of rs5757642 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	-24507
chr22	39747253	39748836	E067	-15988
chr22	39749418	39749798	E067	-15026
chr22	39756071	39756219	E067	-8605
chr22	39759478	39759528	E067	-5296
chr22	39759585	39759639	E067	-5185
chr22	39759655	39759705	E067	-5119
chr22	39759749	39759819	E067	-5005
chr22	39759825	39760379	E067	-4445
chr22	39760450	39760523	E067	-4301
chr22	39760555	39760639	E067	-4185
chr22	39760725	39761343	E067	-3481
chr22	39761374	39761687	E067	-3137
chr22	39761745	39761795	E067	-3029
chr22	39796942	39797016	E067	32118
chr22	39797125	39797194	E067	32301
chr22	39797280	39797320	E067	32456
chr22	39797364	39797418	E067	32540
chr22	39797453	39797503	E067	32629
chr22	39797678	39797734	E067	32854
chr22	39800834	39800978	E067	36010
chr22	39805443	39805507	E067	40619
chr22	39805672	39805773	E067	40848
chr22	39807913	39807993	E067	43089
chr22	39808079	39808159	E067	43255
chr22	39810454	39810622	E067	45630
chr22	39810641	39810702	E067	45817
chr22	39810869	39811312	E067	46045
chr22	39811314	39811374	E067	46490
chr22	39811477	39811531	E067	46653
chr22	39728515	39729151	E068	-35673
chr22	39739329	39739409	E068	-25415
chr22	39739454	39740121	E068	-24703
chr22	39744763	39744848	E068	-19976
chr22	39747253	39748836	E068	-15988
chr22	39758753	39758803	E068	-6021
chr22	39758887	39758967	E068	-5857
chr22	39759014	39759172	E068	-5652
chr22	39759478	39759528	E068	-5296
chr22	39759585	39759639	E068	-5185
chr22	39759655	39759705	E068	-5119
chr22	39759749	39759819	E068	-5005
chr22	39759825	39760379	E068	-4445
chr22	39760450	39760523	E068	-4301
chr22	39760555	39760639	E068	-4185
chr22	39760725	39761343	E068	-3481
chr22	39796942	39797016	E068	32118
chr22	39797125	39797194	E068	32301
chr22	39797280	39797320	E068	32456
chr22	39797364	39797418	E068	32540
chr22	39797453	39797503	E068	32629
chr22	39797678	39797734	E068	32854
chr22	39800834	39800978	E068	36010
chr22	39805443	39805507	E068	40619
chr22	39805672	39805773	E068	40848
chr22	39809797	39809847	E068	44973
chr22	39809936	39810006	E068	45112
chr22	39810285	39810368	E068	45461
chr22	39810454	39810622	E068	45630
chr22	39810641	39810702	E068	45817
chr22	39810869	39811312	E068	46045
chr22	39811314	39811374	E068	46490
chr22	39812365	39812570	E068	47541
chr22	39812572	39812679	E068	47748
chr22	39812786	39812905	E068	47962
chr22	39812991	39813045	E068	48167
chr22	39728515	39729151	E069	-35673
chr22	39739329	39739409	E069	-25415
chr22	39739454	39740121	E069	-24703
chr22	39744763	39744848	E069	-19976
chr22	39758753	39758803	E069	-6021
chr22	39758887	39758967	E069	-5857
chr22	39759014	39759172	E069	-5652
chr22	39759478	39759528	E069	-5296
chr22	39759585	39759639	E069	-5185
chr22	39759655	39759705	E069	-5119
chr22	39759749	39759819	E069	-5005
chr22	39759825	39760379	E069	-4445
chr22	39760450	39760523	E069	-4301
chr22	39760555	39760639	E069	-4185
chr22	39796942	39797016	E069	32118
chr22	39797125	39797194	E069	32301
chr22	39797280	39797320	E069	32456
chr22	39797364	39797418	E069	32540
chr22	39797453	39797503	E069	32629
chr22	39797678	39797734	E069	32854
chr22	39800834	39800978	E069	36010
chr22	39805224	39805264	E069	40400
chr22	39805443	39805507	E069	40619
chr22	39805672	39805773	E069	40848
chr22	39806067	39806150	E069	41243
chr22	39806436	39806603	E069	41612
chr22	39809936	39810006	E069	45112
chr22	39810285	39810368	E069	45461
chr22	39810454	39810622	E069	45630
chr22	39810641	39810702	E069	45817
chr22	39810869	39811312	E069	46045
chr22	39811314	39811374	E069	46490
chr22	39811477	39811531	E069	46653
chr22	39811588	39811638	E069	46764
chr22	39728515	39729151	E070	-35673
chr22	39744594	39744644	E070	-20180
chr22	39744763	39744848	E070	-19976
chr22	39759478	39759528	E070	-5296
chr22	39759585	39759639	E070	-5185
chr22	39759655	39759705	E070	-5119
chr22	39797125	39797194	E070	32301
chr22	39797280	39797320	E070	32456
chr22	39797364	39797418	E070	32540
chr22	39797453	39797503	E070	32629
chr22	39797678	39797734	E070	32854
chr22	39797892	39797966	E070	33068
chr22	39798117	39798172	E070	33293
chr22	39798975	39799023	E070	34151
chr22	39799034	39799078	E070	34210
chr22	39799180	39799264	E070	34356
chr22	39799305	39799355	E070	34481
chr22	39799520	39799587	E070	34696
chr22	39728044	39728226	E071	-36598
chr22	39739454	39740121	E071	-24703
chr22	39744594	39744644	E071	-20180
chr22	39744763	39744848	E071	-19976
chr22	39747253	39748836	E071	-15988
chr22	39749418	39749798	E071	-15026
chr22	39752528	39752755	E071	-12069
chr22	39758115	39758720	E071	-6104
chr22	39758753	39758803	E071	-6021
chr22	39758887	39758967	E071	-5857
chr22	39759014	39759172	E071	-5652
chr22	39759478	39759528	E071	-5296
chr22	39759585	39759639	E071	-5185
chr22	39759655	39759705	E071	-5119
chr22	39759749	39759819	E071	-5005
chr22	39759825	39760379	E071	-4445
chr22	39760450	39760523	E071	-4301
chr22	39760555	39760639	E071	-4185
chr22	39760725	39761343	E071	-3481
chr22	39761374	39761687	E071	-3137
chr22	39761745	39761795	E071	-3029
chr22	39764032	39764205	E071	-619
chr22	39764221	39764274	E071	-550
chr22	39764360	39764425	E071	-399
chr22	39796942	39797016	E071	32118
chr22	39797125	39797194	E071	32301
chr22	39797364	39797418	E071	32540
chr22	39797453	39797503	E071	32629
chr22	39797678	39797734	E071	32854
chr22	39802503	39802558	E071	37679
chr22	39803032	39803116	E071	38208
chr22	39803204	39803265	E071	38380
chr22	39803738	39803788	E071	38914
chr22	39803903	39804100	E071	39079
chr22	39804245	39804490	E071	39421
chr22	39804827	39804884	E071	40003
chr22	39804919	39804972	E071	40095
chr22	39805224	39805264	E071	40400
chr22	39805672	39805773	E071	40848
chr22	39806067	39806150	E071	41243
chr22	39806436	39806603	E071	41612
chr22	39807585	39807671	E071	42761
chr22	39807913	39807993	E071	43089
chr22	39808079	39808159	E071	43255
chr22	39808318	39808963	E071	43494
chr22	39809797	39809847	E071	44973
chr22	39809936	39810006	E071	45112
chr22	39810285	39810368	E071	45461
chr22	39810454	39810622	E071	45630
chr22	39810641	39810702	E071	45817
chr22	39810869	39811312	E071	46045
chr22	39811314	39811374	E071	46490
chr22	39811477	39811531	E071	46653
chr22	39811588	39811638	E071	46764
chr22	39811970	39812014	E071	47146
chr22	39728515	39729151	E072	-35673
chr22	39744763	39744848	E072	-19976
chr22	39755846	39756065	E072	-8759
chr22	39758753	39758803	E072	-6021
chr22	39758887	39758967	E072	-5857
chr22	39759014	39759172	E072	-5652
chr22	39759478	39759528	E072	-5296
chr22	39759585	39759639	E072	-5185
chr22	39759655	39759705	E072	-5119
chr22	39759749	39759819	E072	-5005
chr22	39759825	39760379	E072	-4445
chr22	39760450	39760523	E072	-4301
chr22	39760555	39760639	E072	-4185
chr22	39760725	39761343	E072	-3481
chr22	39805443	39805507	E072	40619
chr22	39805672	39805773	E072	40848
chr22	39806067	39806150	E072	41243
chr22	39806436	39806603	E072	41612
chr22	39807585	39807671	E072	42761
chr22	39807913	39807993	E072	43089
chr22	39808079	39808159	E072	43255
chr22	39809936	39810006	E072	45112
chr22	39810285	39810368	E072	45461
chr22	39810454	39810622	E072	45630
chr22	39810641	39810702	E072	45817
chr22	39810869	39811312	E072	46045
chr22	39811314	39811374	E072	46490
chr22	39739329	39739409	E073	-25415
chr22	39739454	39740121	E073	-24703
chr22	39752528	39752755	E073	-12069
chr22	39752784	39752900	E073	-11924
chr22	39755032	39755076	E073	-9748
chr22	39755279	39755329	E073	-9495
chr22	39755680	39755757	E073	-9067
chr22	39755846	39756065	E073	-8759
chr22	39756071	39756219	E073	-8605
chr22	39756393	39756527	E073	-8297
chr22	39756695	39756820	E073	-8004
chr22	39756898	39757465	E073	-7359
chr22	39757679	39757735	E073	-7089
chr22	39757799	39757905	E073	-6919
chr22	39757992	39758042	E073	-6782
chr22	39758115	39758720	E073	-6104
chr22	39758753	39758803	E073	-6021
chr22	39758887	39758967	E073	-5857
chr22	39759014	39759172	E073	-5652
chr22	39759478	39759528	E073	-5296
chr22	39759585	39759639	E073	-5185
chr22	39759655	39759705	E073	-5119
chr22	39759749	39759819	E073	-5005
chr22	39759825	39760379	E073	-4445
chr22	39760450	39760523	E073	-4301
chr22	39760555	39760639	E073	-4185
chr22	39760725	39761343	E073	-3481
chr22	39761374	39761687	E073	-3137
chr22	39761745	39761795	E073	-3029
chr22	39764032	39764205	E073	-619
chr22	39764221	39764274	E073	-550
chr22	39764360	39764425	E073	-399
chr22	39764479	39765083	E073	0
chr22	39765153	39765234	E073	329
chr22	39765391	39765526	E073	567
chr22	39796942	39797016	E073	32118
chr22	39797125	39797194	E073	32301
chr22	39797280	39797320	E073	32456
chr22	39797364	39797418	E073	32540
chr22	39797453	39797503	E073	32629
chr22	39797678	39797734	E073	32854
chr22	39797892	39797966	E073	33068
chr22	39800834	39800978	E073	36010
chr22	39805443	39805507	E073	40619
chr22	39809936	39810006	E073	45112
chr22	39810285	39810368	E073	45461
chr22	39810454	39810622	E073	45630
chr22	39810641	39810702	E073	45817
chr22	39728515	39729151	E074	-35673
chr22	39739329	39739409	E074	-25415
chr22	39739454	39740121	E074	-24703
chr22	39796942	39797016	E074	32118
chr22	39797125	39797194	E074	32301
chr22	39797280	39797320	E074	32456
chr22	39797364	39797418	E074	32540
chr22	39797453	39797503	E074	32629
chr22	39797678	39797734	E074	32854
chr22	39797892	39797966	E074	33068
chr22	39800834	39800978	E074	36010
chr22	39801024	39801157	E074	36200
chr22	39803903	39804100	E074	39079
chr22	39804245	39804490	E074	39421
chr22	39804827	39804884	E074	40003
chr22	39804919	39804972	E074	40095
chr22	39805224	39805264	E074	40400
chr22	39805443	39805507	E074	40619
chr22	39805672	39805773	E074	40848
chr22	39806067	39806150	E074	41243
chr22	39806436	39806603	E074	41612
chr22	39807585	39807671	E074	42761
chr22	39807913	39807993	E074	43089
chr22	39810285	39810368	E074	45461
chr22	39810454	39810622	E074	45630
chr22	39810641	39810702	E074	45817
chr22	39810869	39811312	E074	46045
chr22	39811314	39811374	E074	46490
chr22	39811477	39811531	E074	46653
chr22	39811588	39811638	E074	46764
chr22	39811970	39812014	E074	47146
chr22	39812240	39812280	E074	47416
chr22	39812365	39812570	E074	47541
chr22	39812572	39812679	E074	47748
chr22	39744763	39744848	E081	-19976
chr22	39747253	39748836	E081	-15988
chr22	39749418	39749798	E081	-15026
chr22	39751905	39751986	E081	-12838
chr22	39752528	39752755	E081	-12069
chr22	39752784	39752900	E081	-11924
chr22	39752903	39753067	E081	-11757
chr22	39753209	39753336	E081	-11488
chr22	39753378	39753424	E081	-11400
chr22	39758115	39758720	E081	-6104
chr22	39758753	39758803	E081	-6021
chr22	39758887	39758967	E081	-5857
chr22	39759014	39759172	E081	-5652
chr22	39759478	39759528	E081	-5296
chr22	39759585	39759639	E081	-5185
chr22	39759655	39759705	E081	-5119
chr22	39759749	39759819	E081	-5005
chr22	39759825	39760379	E081	-4445
chr22	39760450	39760523	E081	-4301
chr22	39760555	39760639	E081	-4185
chr22	39760725	39761343	E081	-3481
chr22	39761374	39761687	E081	-3137
chr22	39761745	39761795	E081	-3029
chr22	39791863	39791956	E081	27039
chr22	39791964	39792018	E081	27140
chr22	39792054	39792275	E081	27230
chr22	39792341	39792438	E081	27517
chr22	39792551	39792655	E081	27727
chr22	39792684	39792740	E081	27860
chr22	39793004	39793202	E081	28180
chr22	39793716	39793770	E081	28892
chr22	39793854	39793904	E081	29030
chr22	39794369	39794410	E081	29545
chr22	39796942	39797016	E081	32118
chr22	39797125	39797194	E081	32301
chr22	39800834	39800978	E081	36010
chr22	39801024	39801157	E081	36200
chr22	39752784	39752900	E082	-11924
chr22	39752903	39753067	E082	-11757
chr22	39753209	39753336	E082	-11488
chr22	39753378	39753424	E082	-11400
chr22	39755846	39756065	E082	-8759
chr22	39756071	39756219	E082	-8605
chr22	39757992	39758042	E082	-6782
chr22	39758115	39758720	E082	-6104
chr22	39758753	39758803	E082	-6021
chr22	39758887	39758967	E082	-5857
chr22	39759014	39759172	E082	-5652
chr22	39759478	39759528	E082	-5296
chr22	39759585	39759639	E082	-5185
chr22	39759655	39759705	E082	-5119
chr22	39759749	39759819	E082	-5005
chr22	39759825	39760379	E082	-4445
chr22	39760450	39760523	E082	-4301
chr22	39760555	39760639	E082	-4185
chr22	39760725	39761343	E082	-3481
chr22	39761374	39761687	E082	-3137
chr22	39761745	39761795	E082	-3029
chr22	39764032	39764205	E082	-619
chr22	39764221	39764274	E082	-550
chr22	39764360	39764425	E082	-399
chr22	39792054	39792275	E082	27230
chr22	39792341	39792438	E082	27517
chr22	39792551	39792655	E082	27727
chr22	39792684	39792740	E082	27860

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	39744862	39747068	E067	-17756
chr22	39784188	39785180	E067	19364
chr22	39795185	39795304	E067	30361
chr22	39795316	39796720	E067	30492
chr22	39744862	39747068	E068	-17756
chr22	39784188	39785180	E068	19364
chr22	39795185	39795304	E068	30361
chr22	39795316	39796720	E068	30492
chr22	39744862	39747068	E069	-17756
chr22	39784188	39785180	E069	19364
chr22	39795185	39795304	E069	30361
chr22	39795316	39796720	E069	30492
chr22	39716596	39716890	E070	-47934
chr22	39744862	39747068	E070	-17756
chr22	39795316	39796720	E070	30492
chr22	39716596	39716890	E071	-47934
chr22	39744862	39747068	E071	-17756
chr22	39784188	39785180	E071	19364
chr22	39795185	39795304	E071	30361
chr22	39795316	39796720	E071	30492
chr22	39716596	39716890	E072	-47934
chr22	39744862	39747068	E072	-17756
chr22	39784188	39785180	E072	19364
chr22	39795185	39795304	E072	30361
chr22	39795316	39796720	E072	30492
chr22	39716596	39716890	E073	-47934
chr22	39744862	39747068	E073	-17756
chr22	39784188	39785180	E073	19364
chr22	39795185	39795304	E073	30361
chr22	39795316	39796720	E073	30492
chr22	39744862	39747068	E074	-17756
chr22	39784188	39785180	E074	19364
chr22	39795185	39795304	E074	30361
chr22	39795316	39796720	E074	30492
chr22	39716596	39716890	E081	-47934
chr22	39744862	39747068	E081	-17756
chr22	39795185	39795304	E081	30361
chr22	39795316	39796720	E081	30492
chr22	39716596	39716890	E082	-47934
chr22	39744862	39747068	E082	-17756
chr22	39795185	39795304	E082	30361
chr22	39795316	39796720	E082	30492