rs1565937

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RYR3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0331 (9920/29946,GnomAD)
T=0299 (8719/29118,TOPMED)
T=0432 (2165/5008,1000G)
T=0290 (1116/3854,ALSPAC)
T=0287 (1066/3708,TWINSUK)

Position: chr15:33603990 (GRCh38.p7) (15q14)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.33603990C>T
GRCh37.p13 chr 15	NC_000015.9:g.33896191C>T

Gene: RYR3, ryanodine receptor 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RYR3 transcript variant 1	NM_001036.4:c.	N/A	Intron Variant
RYR3 transcript variant 2	NM_001243996.2:c.	N/A	Intron Variant
RYR3 transcript variant X9	XM_011521880.2:c.	N/A	Intron Variant
RYR3 transcript variant X1	XM_017022468.1:c.	N/A	Intron Variant
RYR3 transcript variant X2	XM_017022469.1:c.	N/A	Intron Variant
RYR3 transcript variant X3	XM_017022470.1:c.	N/A	Intron Variant
RYR3 transcript variant X4	XM_017022471.1:c.	N/A	Intron Variant
RYR3 transcript variant X5	XM_017022472.1:c.	N/A	Intron Variant
RYR3 transcript variant X7	XM_017022473.1:c.	N/A	Intron Variant
RYR3 transcript variant X8	XM_017022474.1:c.	N/A	Intron Variant
RYR3 transcript variant X10	XM_017022475.1:c.	N/A	Intron Variant
RYR3 transcript variant X11	XM_017022476.1:c.	N/A	Intron Variant
RYR3 transcript variant X13	XM_017022477.1:c.	N/A	Intron Variant
RYR3 transcript variant X12	XR_001751369.1:n.	N/A	Intron Variant
RYR3 transcript variant X14	XR_001751370.1:n.	N/A	Intron Variant
RYR3 transcript variant X14	XR_001751371.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.781	T=0.219
1000Genomes	American	Sub	694	C=0.550	T=0.450
1000Genomes	East Asian	Sub	1008	C=0.242	T=0.758
1000Genomes	Europe	Sub	1006	C=0.677	T=0.323
1000Genomes	Global	Study-wide	5008	C=0.568	T=0.432
1000Genomes	South Asian	Sub	978	C=0.520	T=0.480
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.710	T=0.290
The Genome Aggregation Database	African	Sub	8726	C=0.747	T=0.253
The Genome Aggregation Database	American	Sub	836	C=0.550	T=0.450
The Genome Aggregation Database	East Asian	Sub	1614	C=0.271	T=0.729
The Genome Aggregation Database	Europe	Sub	18468	C=0.671	T=0.328
The Genome Aggregation Database	Global	Study-wide	29946	C=0.668	T=0.331
The Genome Aggregation Database	Other	Sub	302	C=0.690	T=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.700	T=0.299
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.713	T=0.287

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
rs1565937	0.000174	alcohol dependence	20201924

eQTL of rs1565937 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 rs1565937 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 )
chr15	33872448	33872691	E067	-23500
chr15	33872696	33873206	E067	-22985
chr15	33873244	33873789	E067	-22402
chr15	33851247	33851441	E068	-44750
chr15	33851500	33851716	E068	-44475
chr15	33872696	33873206	E068	-22985
chr15	33931797	33931889	E070	35606
chr15	33932904	33932954	E070	36713
chr15	33933296	33933465	E070	37105
chr15	33931797	33931889	E081	35606