rs7565777

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC105373947 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0310 (9282/29880,GnomAD)
G=0397 (11561/29118,TOPMED)
G=0367 (1839/5008,1000G)
G=0208 (803/3854,ALSPAC)
G=0196 (725/3708,TWINSUK)

Position: chr2:236607651 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 125 Enhancers around

Promoter: 45 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.236607651A>G
GRCh37.p13 chr 2	NC_000002.11:g.237516294A>G

Gene: LOC105373947, uncharacterized LOC105373947(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373947 transcript variant X1	XR_924020.2:n.	N/A	Intron Variant
LOC105373947 transcript variant X2	XR_924021.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.289	G=0.711
1000Genomes	American	Sub	694	A=0.830	G=0.170
1000Genomes	East Asian	Sub	1008	A=0.789	G=0.211
1000Genomes	Europe	Sub	1006	A=0.786	G=0.214
1000Genomes	Global	Study-wide	5008	A=0.633	G=0.367
1000Genomes	South Asian	Sub	978	A=0.640	G=0.360
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.792	G=0.208
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.603	G=0.397
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.804	G=0.196

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs7565777	3.6E-06	alcohol dependence (age at onset)	24962325

eQTL of rs7565777 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 rs7565777 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 )
chr2	237481042	237481559	E067	-34735
chr2	237481570	237482025	E067	-34269
chr2	237487622	237487975	E067	-28319
chr2	237488021	237488075	E067	-28219
chr2	237488238	237488418	E067	-27876
chr2	237488500	237488907	E067	-27387
chr2	237538984	237539374	E067	22690
chr2	237468059	237468109	E068	-48185
chr2	237484754	237485097	E068	-31197
chr2	237485162	237485354	E068	-30940
chr2	237485667	237485904	E068	-30390
chr2	237486488	237487091	E068	-29203
chr2	237522085	237522176	E068	5791
chr2	237534685	237534740	E068	18391
chr2	237538984	237539374	E068	22690
chr2	237539431	237539520	E068	23137
chr2	237539626	237539827	E068	23332
chr2	237487622	237487975	E069	-28319
chr2	237488021	237488075	E069	-28219
chr2	237488238	237488418	E069	-27876
chr2	237488500	237488907	E069	-27387
chr2	237538984	237539374	E069	22690
chr2	237539431	237539520	E069	23137
chr2	237539626	237539827	E069	23332
chr2	237539863	237540345	E069	23569
chr2	237540358	237540459	E069	24064
chr2	237485162	237485354	E070	-30940
chr2	237485667	237485904	E070	-30390
chr2	237524722	237525153	E070	8428
chr2	237525341	237525551	E070	9047
chr2	237525752	237526482	E070	9458
chr2	237526554	237526634	E070	10260
chr2	237534685	237534740	E070	18391
chr2	237534920	237535000	E070	18626
chr2	237539626	237539827	E070	23332
chr2	237539863	237540345	E070	23569
chr2	237466643	237466811	E071	-49483
chr2	237466934	237467036	E071	-49258
chr2	237482579	237482754	E071	-33540
chr2	237482791	237482927	E071	-33367
chr2	237484754	237485097	E071	-31197
chr2	237485162	237485354	E071	-30940
chr2	237485667	237485904	E071	-30390
chr2	237487273	237487328	E071	-28966
chr2	237487622	237487975	E071	-28319
chr2	237488021	237488075	E071	-28219
chr2	237488238	237488418	E071	-27876
chr2	237488500	237488907	E071	-27387
chr2	237521857	237521932	E071	5563
chr2	237522085	237522176	E071	5791
chr2	237522433	237522641	E071	6139
chr2	237534373	237534518	E071	18079
chr2	237538984	237539374	E071	22690
chr2	237539431	237539520	E071	23137
chr2	237481570	237482025	E072	-34269
chr2	237482137	237482275	E072	-34019
chr2	237482332	237482520	E072	-33774
chr2	237482579	237482754	E072	-33540
chr2	237487273	237487328	E072	-28966
chr2	237487622	237487975	E072	-28319
chr2	237488021	237488075	E072	-28219
chr2	237488238	237488418	E072	-27876
chr2	237488500	237488907	E072	-27387
chr2	237490341	237490483	E072	-25811
chr2	237521857	237521932	E072	5563
chr2	237522085	237522176	E072	5791
chr2	237522433	237522641	E072	6139
chr2	237534373	237534518	E072	18079
chr2	237538984	237539374	E072	22690
chr2	237539431	237539520	E072	23137
chr2	237539626	237539827	E072	23332
chr2	237539863	237540345	E072	23569
chr2	237540358	237540459	E072	24064
chr2	237481570	237482025	E073	-34269
chr2	237482137	237482275	E073	-34019
chr2	237482332	237482520	E073	-33774
chr2	237487273	237487328	E073	-28966
chr2	237466643	237466811	E074	-49483
chr2	237488021	237488075	E074	-28219
chr2	237488238	237488418	E074	-27876
chr2	237488500	237488907	E074	-27387
chr2	237521857	237521932	E074	5563
chr2	237522085	237522176	E074	5791
chr2	237522433	237522641	E074	6139
chr2	237534373	237534518	E074	18079
chr2	237538984	237539374	E074	22690
chr2	237539431	237539520	E074	23137
chr2	237539626	237539827	E074	23332
chr2	237539863	237540345	E074	23569
chr2	237540358	237540459	E074	24064
chr2	237483169	237483758	E081	-32536
chr2	237483759	237483822	E081	-32472
chr2	237484300	237484542	E081	-31752
chr2	237484754	237485097	E081	-31197
chr2	237485162	237485354	E081	-30940
chr2	237488238	237488418	E081	-27876
chr2	237488500	237488907	E081	-27387
chr2	237497942	237498290	E081	-18004
chr2	237521497	237521694	E081	5203
chr2	237521857	237521932	E081	5563
chr2	237522085	237522176	E081	5791
chr2	237522433	237522641	E081	6139
chr2	237523023	237523127	E081	6729
chr2	237523281	237523441	E081	6987
chr2	237523633	237523683	E081	7339
chr2	237524722	237525153	E081	8428
chr2	237525341	237525551	E081	9047
chr2	237525752	237526482	E081	9458
chr2	237526554	237526634	E081	10260
chr2	237538984	237539374	E081	22690
chr2	237539431	237539520	E081	23137
chr2	237539626	237539827	E081	23332
chr2	237539863	237540345	E081	23569
chr2	237540358	237540459	E081	24064
chr2	237496250	237496385	E082	-19909
chr2	237521497	237521694	E082	5203
chr2	237521857	237521932	E082	5563
chr2	237522085	237522176	E082	5791
chr2	237522433	237522641	E082	6139
chr2	237523023	237523127	E082	6729
chr2	237523281	237523441	E082	6987
chr2	237523633	237523683	E082	7339
chr2	237525341	237525551	E082	9047
chr2	237525752	237526482	E082	9458
chr2	237540358	237540459	E082	24064

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	237476609	237479749	E067	-36545
chr2	237479804	237480012	E067	-36282
chr2	237480080	237480193	E067	-36101
chr2	237480285	237480401	E067	-35893
chr2	237476012	237476545	E068	-39749
chr2	237476609	237479749	E068	-36545
chr2	237479804	237480012	E068	-36282
chr2	237480080	237480193	E068	-36101
chr2	237480285	237480401	E068	-35893
chr2	237480652	237480707	E068	-35587
chr2	237480715	237480784	E068	-35510
chr2	237476609	237479749	E069	-36545
chr2	237479804	237480012	E069	-36282
chr2	237480080	237480193	E069	-36101
chr2	237480285	237480401	E069	-35893
chr2	237480652	237480707	E069	-35587
chr2	237480715	237480784	E069	-35510
chr2	237480080	237480193	E070	-36101
chr2	237480285	237480401	E070	-35893
chr2	237480652	237480707	E070	-35587
chr2	237480715	237480784	E070	-35510
chr2	237476609	237479749	E071	-36545
chr2	237479804	237480012	E071	-36282
chr2	237480080	237480193	E071	-36101
chr2	237480285	237480401	E071	-35893
chr2	237480652	237480707	E071	-35587
chr2	237480715	237480784	E071	-35510
chr2	237476609	237479749	E072	-36545
chr2	237479804	237480012	E072	-36282
chr2	237480080	237480193	E072	-36101
chr2	237476012	237476545	E073	-39749
chr2	237476609	237479749	E073	-36545
chr2	237479804	237480012	E073	-36282
chr2	237480080	237480193	E073	-36101
chr2	237476609	237479749	E074	-36545
chr2	237479804	237480012	E074	-36282
chr2	237480080	237480193	E074	-36101
chr2	237480285	237480401	E074	-35893
chr2	237480652	237480707	E074	-35587
chr2	237480715	237480784	E074	-35510
chr2	237476609	237479749	E082	-36545
chr2	237479804	237480012	E082	-36282
chr2	237480285	237480401	E082	-35893
chr2	237480652	237480707	E082	-35587
chr2	237480715	237480784	E082	-35510