rs2496320

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

EFHD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0193 (5766/29868,GnomAD)
C=0258 (7530/29118,TOPMED)
C=0198 (991/5008,1000G)
C=0125 (483/3854,ALSPAC)
C=0126 (467/3708,TWINSUK)

Position: chr1:15417775 (GRCh38.p7) (1p36.21)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 138 Enhancers around

Promoter: 33 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.15417775T>C
GRCh37.p13 chr 1	NC_000001.10:g.15744271T>C

Gene: EFHD2, EF-hand domain family member D2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EFHD2 transcript	NM_024329.5:c.	N/A	Intron Variant
EFHD2 transcript variant X1	XM_005246000.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.555	C=0.445
1000Genomes	American	Sub	694	T=0.860	C=0.140
1000Genomes	East Asian	Sub	1008	T=0.892	C=0.108
1000Genomes	Europe	Sub	1006	T=0.885	C=0.115
1000Genomes	Global	Study-wide	5008	T=0.802	C=0.198
1000Genomes	South Asian	Sub	978	T=0.920	C=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.875	C=0.125
The Genome Aggregation Database	African	Sub	8680	T=0.589	C=0.411
The Genome Aggregation Database	American	Sub	834	T=0.830	C=0.170
The Genome Aggregation Database	East Asian	Sub	1614	T=0.906	C=0.094
The Genome Aggregation Database	Europe	Sub	18438	T=0.899	C=0.100
The Genome Aggregation Database	Global	Study-wide	29868	T=0.807	C=0.193
The Genome Aggregation Database	Other	Sub	302	T=0.830	C=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.741	C=0.258
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.874	C=0.126

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
rs2496320	0.000526	alcohol dependence	20201924

eQTL of rs2496320 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 rs2496320 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 )
chr1	15710151	15710275	E067	-33996
chr1	15710341	15710548	E067	-33723
chr1	15711444	15711580	E067	-32691
chr1	15733243	15734285	E067	-9986
chr1	15739412	15739597	E067	-4674
chr1	15739867	15740217	E067	-4054
chr1	15740258	15740338	E067	-3933
chr1	15740624	15740877	E067	-3394
chr1	15745394	15745609	E067	1123
chr1	15745779	15745876	E067	1508
chr1	15746305	15746345	E067	2034
chr1	15710151	15710275	E068	-33996
chr1	15710341	15710548	E068	-33723
chr1	15711955	15712013	E068	-32258
chr1	15739412	15739597	E068	-4674
chr1	15739631	15739787	E068	-4484
chr1	15739867	15740217	E068	-4054
chr1	15742294	15743398	E068	-873
chr1	15745126	15745204	E068	855
chr1	15745394	15745609	E068	1123
chr1	15745779	15745876	E068	1508
chr1	15753811	15753933	E068	9540
chr1	15753940	15754109	E068	9669
chr1	15697058	15697144	E069	-47127
chr1	15710341	15710548	E069	-33723
chr1	15711955	15712013	E069	-32258
chr1	15712330	15712529	E069	-31742
chr1	15739867	15740217	E069	-4054
chr1	15740258	15740338	E069	-3933
chr1	15740624	15740877	E069	-3394
chr1	15740974	15741472	E069	-2799
chr1	15745126	15745204	E069	855
chr1	15745394	15745609	E069	1123
chr1	15745779	15745876	E069	1508
chr1	15697223	15698350	E070	-45921
chr1	15698384	15698595	E070	-45676
chr1	15706858	15706916	E070	-37355
chr1	15707144	15707254	E070	-37017
chr1	15707584	15707624	E070	-36647
chr1	15707790	15707846	E070	-36425
chr1	15710151	15710275	E070	-33996
chr1	15710341	15710548	E070	-33723
chr1	15711955	15712013	E070	-32258
chr1	15712330	15712529	E070	-31742
chr1	15739412	15739597	E070	-4674
chr1	15739631	15739787	E070	-4484
chr1	15745779	15745876	E070	1508
chr1	15758173	15758273	E070	13902
chr1	15758324	15758497	E070	14053
chr1	15758529	15758594	E070	14258
chr1	15697223	15698350	E071	-45921
chr1	15710341	15710548	E071	-33723
chr1	15711444	15711580	E071	-32691
chr1	15711955	15712013	E071	-32258
chr1	15712330	15712529	E071	-31742
chr1	15733243	15734285	E071	-9986
chr1	15739867	15740217	E071	-4054
chr1	15740974	15741472	E071	-2799
chr1	15742294	15743398	E071	-873
chr1	15745126	15745204	E071	855
chr1	15745394	15745609	E071	1123
chr1	15745779	15745876	E071	1508
chr1	15786520	15786700	E071	42249
chr1	15710341	15710548	E072	-33723
chr1	15711955	15712013	E072	-32258
chr1	15712330	15712529	E072	-31742
chr1	15734470	15734687	E072	-9584
chr1	15739412	15739597	E072	-4674
chr1	15739631	15739787	E072	-4484
chr1	15739867	15740217	E072	-4054
chr1	15740258	15740338	E072	-3933
chr1	15740624	15740877	E072	-3394
chr1	15745126	15745204	E072	855
chr1	15745394	15745609	E072	1123
chr1	15745779	15745876	E072	1508
chr1	15747510	15747791	E072	3239
chr1	15747994	15748529	E072	3723
chr1	15749728	15750073	E072	5457
chr1	15697058	15697144	E073	-47127
chr1	15697223	15698350	E073	-45921
chr1	15710151	15710275	E073	-33996
chr1	15710341	15710548	E073	-33723
chr1	15711444	15711580	E073	-32691
chr1	15745126	15745204	E073	855
chr1	15745394	15745609	E073	1123
chr1	15745779	15745876	E073	1508
chr1	15746305	15746345	E073	2034
chr1	15749728	15750073	E073	5457
chr1	15697058	15697144	E074	-47127
chr1	15710341	15710548	E074	-33723
chr1	15711444	15711580	E074	-32691
chr1	15711955	15712013	E074	-32258
chr1	15739867	15740217	E074	-4054
chr1	15740258	15740338	E074	-3933
chr1	15697223	15698350	E081	-45921
chr1	15698384	15698595	E081	-45676
chr1	15698612	15698681	E081	-45590
chr1	15698714	15698935	E081	-45336
chr1	15699063	15699107	E081	-45164
chr1	15699120	15699228	E081	-45043
chr1	15699236	15699355	E081	-44916
chr1	15707584	15707624	E081	-36647
chr1	15707790	15707846	E081	-36425
chr1	15709417	15709457	E081	-34814
chr1	15709663	15709737	E081	-34534
chr1	15710151	15710275	E081	-33996
chr1	15710341	15710548	E081	-33723
chr1	15712330	15712529	E081	-31742
chr1	15718003	15718118	E081	-26153
chr1	15739412	15739597	E081	-4674
chr1	15739631	15739787	E081	-4484
chr1	15739867	15740217	E081	-4054
chr1	15740258	15740338	E081	-3933
chr1	15740624	15740877	E081	-3394
chr1	15745126	15745204	E081	855
chr1	15745394	15745609	E081	1123
chr1	15745779	15745876	E081	1508
chr1	15753183	15753794	E081	8912
chr1	15753811	15753933	E081	9540
chr1	15753940	15754109	E081	9669
chr1	15758647	15759704	E081	14376
chr1	15786520	15786700	E081	42249
chr1	15697223	15698350	E082	-45921
chr1	15698714	15698935	E082	-45336
chr1	15699063	15699107	E082	-45164
chr1	15699120	15699228	E082	-45043
chr1	15706858	15706916	E082	-37355
chr1	15707144	15707254	E082	-37017
chr1	15709663	15709737	E082	-34534
chr1	15710151	15710275	E082	-33996
chr1	15710341	15710548	E082	-33723
chr1	15727786	15728363	E082	-15908
chr1	15739412	15739597	E082	-4674
chr1	15745126	15745204	E082	855
chr1	15745394	15745609	E082	1123
chr1	15745779	15745876	E082	1508
chr1	15758324	15758497	E082	14053
chr1	15758529	15758594	E082	14258

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	15735070	15736777	E067	-7494
chr1	15736830	15736878	E067	-7393
chr1	15736909	15736966	E067	-7305
chr1	15737034	15737721	E067	-6550
chr1	15735070	15736777	E068	-7494
chr1	15736830	15736878	E068	-7393
chr1	15736909	15736966	E068	-7305
chr1	15737034	15737721	E068	-6550
chr1	15735070	15736777	E069	-7494
chr1	15736830	15736878	E069	-7393
chr1	15736909	15736966	E069	-7305
chr1	15737034	15737721	E069	-6550
chr1	15735070	15736777	E070	-7494
chr1	15735070	15736777	E071	-7494
chr1	15736830	15736878	E071	-7393
chr1	15736909	15736966	E071	-7305
chr1	15737034	15737721	E071	-6550
chr1	15735070	15736777	E072	-7494
chr1	15736830	15736878	E072	-7393
chr1	15736909	15736966	E072	-7305
chr1	15737034	15737721	E072	-6550
chr1	15735070	15736777	E073	-7494
chr1	15736830	15736878	E073	-7393
chr1	15736909	15736966	E073	-7305
chr1	15737034	15737721	E073	-6550
chr1	15735070	15736777	E074	-7494
chr1	15736830	15736878	E074	-7393
chr1	15736909	15736966	E074	-7305
chr1	15737034	15737721	E074	-6550
chr1	15735070	15736777	E082	-7494
chr1	15736830	15736878	E082	-7393
chr1	15736909	15736966	E082	-7305
chr1	15737034	15737721	E082	-6550