rs2496321

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

EFHD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0267 (8002/29954,GnomAD)
C=0323 (9404/29118,TOPMED)
C=0301 (1509/5008,1000G)
C=0236 (911/3854,ALSPAC)
C=0234 (867/3708,TWINSUK)

Position: chr1:15417388 (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.15417388A>C
GRCh37.p13 chr 1	NC_000001.10:g.15743884A>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	A=0.545	C=0.455
1000Genomes	American	Sub	694	A=0.790	C=0.210
1000Genomes	East Asian	Sub	1008	A=0.796	C=0.204
1000Genomes	Europe	Sub	1006	A=0.761	C=0.239
1000Genomes	Global	Study-wide	5008	A=0.699	C=0.301
1000Genomes	South Asian	Sub	978	A=0.680	C=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.764	C=0.236
The Genome Aggregation Database	African	Sub	8714	A=0.566	C=0.434
The Genome Aggregation Database	American	Sub	836	A=0.790	C=0.210
The Genome Aggregation Database	East Asian	Sub	1620	A=0.810	C=0.190
The Genome Aggregation Database	Europe	Sub	18482	A=0.802	C=0.197
The Genome Aggregation Database	Global	Study-wide	29954	A=0.732	C=0.267
The Genome Aggregation Database	Other	Sub	302	A=0.740	C=0.260
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.677	C=0.323
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.766	C=0.234

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
rs2496321	0.000275	alcohol dependence	20201924

eQTL of rs2496321 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 rs2496321 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	-33609
chr1	15710341	15710548	E067	-33336
chr1	15711444	15711580	E067	-32304
chr1	15733243	15734285	E067	-9599
chr1	15739412	15739597	E067	-4287
chr1	15739867	15740217	E067	-3667
chr1	15740258	15740338	E067	-3546
chr1	15740624	15740877	E067	-3007
chr1	15745394	15745609	E067	1510
chr1	15745779	15745876	E067	1895
chr1	15746305	15746345	E067	2421
chr1	15710151	15710275	E068	-33609
chr1	15710341	15710548	E068	-33336
chr1	15711955	15712013	E068	-31871
chr1	15739412	15739597	E068	-4287
chr1	15739631	15739787	E068	-4097
chr1	15739867	15740217	E068	-3667
chr1	15742294	15743398	E068	-486
chr1	15745126	15745204	E068	1242
chr1	15745394	15745609	E068	1510
chr1	15745779	15745876	E068	1895
chr1	15753811	15753933	E068	9927
chr1	15753940	15754109	E068	10056
chr1	15697058	15697144	E069	-46740
chr1	15710341	15710548	E069	-33336
chr1	15711955	15712013	E069	-31871
chr1	15712330	15712529	E069	-31355
chr1	15739867	15740217	E069	-3667
chr1	15740258	15740338	E069	-3546
chr1	15740624	15740877	E069	-3007
chr1	15740974	15741472	E069	-2412
chr1	15745126	15745204	E069	1242
chr1	15745394	15745609	E069	1510
chr1	15745779	15745876	E069	1895
chr1	15697223	15698350	E070	-45534
chr1	15698384	15698595	E070	-45289
chr1	15706858	15706916	E070	-36968
chr1	15707144	15707254	E070	-36630
chr1	15707584	15707624	E070	-36260
chr1	15707790	15707846	E070	-36038
chr1	15710151	15710275	E070	-33609
chr1	15710341	15710548	E070	-33336
chr1	15711955	15712013	E070	-31871
chr1	15712330	15712529	E070	-31355
chr1	15739412	15739597	E070	-4287
chr1	15739631	15739787	E070	-4097
chr1	15745779	15745876	E070	1895
chr1	15758173	15758273	E070	14289
chr1	15758324	15758497	E070	14440
chr1	15758529	15758594	E070	14645
chr1	15697223	15698350	E071	-45534
chr1	15710341	15710548	E071	-33336
chr1	15711444	15711580	E071	-32304
chr1	15711955	15712013	E071	-31871
chr1	15712330	15712529	E071	-31355
chr1	15733243	15734285	E071	-9599
chr1	15739867	15740217	E071	-3667
chr1	15740974	15741472	E071	-2412
chr1	15742294	15743398	E071	-486
chr1	15745126	15745204	E071	1242
chr1	15745394	15745609	E071	1510
chr1	15745779	15745876	E071	1895
chr1	15786520	15786700	E071	42636
chr1	15710341	15710548	E072	-33336
chr1	15711955	15712013	E072	-31871
chr1	15712330	15712529	E072	-31355
chr1	15734470	15734687	E072	-9197
chr1	15739412	15739597	E072	-4287
chr1	15739631	15739787	E072	-4097
chr1	15739867	15740217	E072	-3667
chr1	15740258	15740338	E072	-3546
chr1	15740624	15740877	E072	-3007
chr1	15745126	15745204	E072	1242
chr1	15745394	15745609	E072	1510
chr1	15745779	15745876	E072	1895
chr1	15747510	15747791	E072	3626
chr1	15747994	15748529	E072	4110
chr1	15749728	15750073	E072	5844
chr1	15697058	15697144	E073	-46740
chr1	15697223	15698350	E073	-45534
chr1	15710151	15710275	E073	-33609
chr1	15710341	15710548	E073	-33336
chr1	15711444	15711580	E073	-32304
chr1	15745126	15745204	E073	1242
chr1	15745394	15745609	E073	1510
chr1	15745779	15745876	E073	1895
chr1	15746305	15746345	E073	2421
chr1	15749728	15750073	E073	5844
chr1	15697058	15697144	E074	-46740
chr1	15710341	15710548	E074	-33336
chr1	15711444	15711580	E074	-32304
chr1	15711955	15712013	E074	-31871
chr1	15739867	15740217	E074	-3667
chr1	15740258	15740338	E074	-3546
chr1	15697223	15698350	E081	-45534
chr1	15698384	15698595	E081	-45289
chr1	15698612	15698681	E081	-45203
chr1	15698714	15698935	E081	-44949
chr1	15699063	15699107	E081	-44777
chr1	15699120	15699228	E081	-44656
chr1	15699236	15699355	E081	-44529
chr1	15707584	15707624	E081	-36260
chr1	15707790	15707846	E081	-36038
chr1	15709417	15709457	E081	-34427
chr1	15709663	15709737	E081	-34147
chr1	15710151	15710275	E081	-33609
chr1	15710341	15710548	E081	-33336
chr1	15712330	15712529	E081	-31355
chr1	15718003	15718118	E081	-25766
chr1	15739412	15739597	E081	-4287
chr1	15739631	15739787	E081	-4097
chr1	15739867	15740217	E081	-3667
chr1	15740258	15740338	E081	-3546
chr1	15740624	15740877	E081	-3007
chr1	15745126	15745204	E081	1242
chr1	15745394	15745609	E081	1510
chr1	15745779	15745876	E081	1895
chr1	15753183	15753794	E081	9299
chr1	15753811	15753933	E081	9927
chr1	15753940	15754109	E081	10056
chr1	15758647	15759704	E081	14763
chr1	15786520	15786700	E081	42636
chr1	15697223	15698350	E082	-45534
chr1	15698714	15698935	E082	-44949
chr1	15699063	15699107	E082	-44777
chr1	15699120	15699228	E082	-44656
chr1	15706858	15706916	E082	-36968
chr1	15707144	15707254	E082	-36630
chr1	15709663	15709737	E082	-34147
chr1	15710151	15710275	E082	-33609
chr1	15710341	15710548	E082	-33336
chr1	15727786	15728363	E082	-15521
chr1	15739412	15739597	E082	-4287
chr1	15745126	15745204	E082	1242
chr1	15745394	15745609	E082	1510
chr1	15745779	15745876	E082	1895
chr1	15758324	15758497	E082	14440
chr1	15758529	15758594	E082	14645

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	15735070	15736777	E067	-7107
chr1	15736830	15736878	E067	-7006
chr1	15736909	15736966	E067	-6918
chr1	15737034	15737721	E067	-6163
chr1	15735070	15736777	E068	-7107
chr1	15736830	15736878	E068	-7006
chr1	15736909	15736966	E068	-6918
chr1	15737034	15737721	E068	-6163
chr1	15735070	15736777	E069	-7107
chr1	15736830	15736878	E069	-7006
chr1	15736909	15736966	E069	-6918
chr1	15737034	15737721	E069	-6163
chr1	15735070	15736777	E070	-7107
chr1	15735070	15736777	E071	-7107
chr1	15736830	15736878	E071	-7006
chr1	15736909	15736966	E071	-6918
chr1	15737034	15737721	E071	-6163
chr1	15735070	15736777	E072	-7107
chr1	15736830	15736878	E072	-7006
chr1	15736909	15736966	E072	-6918
chr1	15737034	15737721	E072	-6163
chr1	15735070	15736777	E073	-7107
chr1	15736830	15736878	E073	-7006
chr1	15736909	15736966	E073	-6918
chr1	15737034	15737721	E073	-6163
chr1	15735070	15736777	E074	-7107
chr1	15736830	15736878	E074	-7006
chr1	15736909	15736966	E074	-6918
chr1	15737034	15737721	E074	-6163
chr1	15735070	15736777	E082	-7107
chr1	15736830	15736878	E082	-7006
chr1	15736909	15736966	E082	-6918
chr1	15737034	15737721	E082	-6163