rs1889925

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

AK4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0270 (8101/29946,GnomAD)
A=0281 (8206/29118,TOPMED)
A=0404 (2025/5008,1000G)
A=0220 (847/3854,ALSPAC)
A=0219 (813/3708,TWINSUK)

Position: chr1:65221873 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 294 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.65221873G>A
GRCh38.p7 chr 1	NC_000001.11:g.65221873G>T
GRCh37.p13 chr 1	NC_000001.10:g.65687556G>A
GRCh37.p13 chr 1	NC_000001.10:g.65687556G>T

Gene: AK4, adenylate kinase 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AK4 transcript variant 1	NM_001005353.2:c.	N/A	Intron Variant
AK4 transcript variant 2	NM_013410.3:c.	N/A	Intron Variant
AK4 transcript variant 3	NM_203464.2:c.	N/A	Intron Variant
AK4 transcript variant X1	XM_017000612.1:c.	N/A	Intron Variant
AK4 transcript variant X1	XM_017000613.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.662	A=0.338
1000Genomes	American	Sub	694	G=0.670	A=0.330
1000Genomes	East Asian	Sub	1008	G=0.283	A=0.717
1000Genomes	Europe	Sub	1006	G=0.798	A=0.202
1000Genomes	Global	Study-wide	5008	G=0.596	A=0.404
1000Genomes	South Asian	Sub	978	G=0.570	A=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.780	A=0.220
The Genome Aggregation Database	African	Sub	8714	G=0.674	A=0.326
The Genome Aggregation Database	American	Sub	836	G=0.660	A=0.34,
The Genome Aggregation Database	East Asian	Sub	1608	G=0.294	A=0.706
The Genome Aggregation Database	Europe	Sub	18486	G=0.796	A=0.203
The Genome Aggregation Database	Global	Study-wide	29946	G=0.729	A=0.270
The Genome Aggregation Database	Other	Sub	302	G=0.750	A=0.25,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.718	A=0.281
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.781	A=0.219

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs1889925	0.000823	alcohol consumption (maxi-drinks)	24277619

eQTL of rs1889925 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 rs1889925 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	112446520	112446577	E067	-39374
chr1	112446628	112446711	E067	-39240
chr1	112447054	112447465	E067	-38486
chr1	112447553	112447841	E067	-38110
chr1	112448053	112448114	E067	-37837
chr1	112449689	112449759	E067	-36192
chr1	112450076	112450213	E067	-35738
chr1	112450697	112450914	E067	-35037
chr1	112451707	112452111	E067	-33840
chr1	112462702	112463337	E067	-22614
chr1	112463442	112463510	E067	-22441
chr1	112463593	112463664	E067	-22287
chr1	112464059	112464119	E067	-21832
chr1	112464605	112464835	E067	-21116
chr1	112490897	112491073	E067	4946
chr1	112491243	112491747	E067	5292
chr1	112503755	112503909	E067	17804
chr1	112504005	112504170	E067	18054
chr1	112504479	112504933	E067	18528
chr1	112506618	112506901	E067	20667
chr1	112506910	112507040	E067	20959
chr1	112507087	112507208	E067	21136
chr1	112446520	112446577	E068	-39374
chr1	112446628	112446711	E068	-39240
chr1	112447054	112447465	E068	-38486
chr1	112447553	112447841	E068	-38110
chr1	112448053	112448114	E068	-37837
chr1	112451707	112452111	E068	-33840
chr1	112452297	112452404	E068	-33547
chr1	112453782	112453971	E068	-31980
chr1	112463442	112463510	E068	-22441
chr1	112463593	112463664	E068	-22287
chr1	112464059	112464119	E068	-21832
chr1	112464605	112464835	E068	-21116
chr1	112490897	112491073	E068	4946
chr1	112498538	112498669	E068	12587
chr1	112498671	112498859	E068	12720
chr1	112498867	112499005	E068	12916
chr1	112501645	112501796	E068	15694
chr1	112503755	112503909	E068	17804
chr1	112504005	112504170	E068	18054
chr1	112504479	112504933	E068	18528
chr1	112506418	112506504	E068	20467
chr1	112506618	112506901	E068	20667
chr1	112506910	112507040	E068	20959
chr1	112507087	112507208	E068	21136
chr1	112530016	112530098	E068	44065
chr1	112445917	112445998	E069	-39953
chr1	112446520	112446577	E069	-39374
chr1	112446628	112446711	E069	-39240
chr1	112447054	112447465	E069	-38486
chr1	112447553	112447841	E069	-38110
chr1	112448053	112448114	E069	-37837
chr1	112451707	112452111	E069	-33840
chr1	112452297	112452404	E069	-33547
chr1	112453782	112453971	E069	-31980
chr1	112463442	112463510	E069	-22441
chr1	112463593	112463664	E069	-22287
chr1	112464059	112464119	E069	-21832
chr1	112464605	112464835	E069	-21116
chr1	112490897	112491073	E069	4946
chr1	112503755	112503909	E069	17804
chr1	112504005	112504170	E069	18054
chr1	112504479	112504933	E069	18528
chr1	112506418	112506504	E069	20467
chr1	112506618	112506901	E069	20667
chr1	112506910	112507040	E069	20959
chr1	112507087	112507208	E069	21136
chr1	112535109	112535527	E069	49158
chr1	112437768	112437877	E070	-48074
chr1	112438157	112438449	E070	-47502
chr1	112438528	112438706	E070	-47245
chr1	112446520	112446577	E070	-39374
chr1	112446628	112446711	E070	-39240
chr1	112447054	112447465	E070	-38486
chr1	112447553	112447841	E070	-38110
chr1	112448053	112448114	E070	-37837
chr1	112450076	112450213	E070	-35738
chr1	112450697	112450914	E070	-35037
chr1	112452297	112452404	E070	-33547
chr1	112453782	112453971	E070	-31980
chr1	112454489	112454768	E070	-31183
chr1	112454900	112455016	E070	-30935
chr1	112462702	112463337	E070	-22614
chr1	112463442	112463510	E070	-22441
chr1	112463593	112463664	E070	-22287
chr1	112464059	112464119	E070	-21832
chr1	112464605	112464835	E070	-21116
chr1	112471509	112471602	E070	-14349
chr1	112472501	112472741	E070	-13210
chr1	112473048	112473243	E070	-12708
chr1	112476436	112476551	E070	-9400
chr1	112477886	112478063	E070	-7888
chr1	112478245	112478363	E070	-7588
chr1	112479785	112480119	E070	-5832
chr1	112485754	112486048	E070	0
chr1	112486464	112486547	E070	513
chr1	112486592	112486690	E070	641
chr1	112487847	112487912	E070	1896
chr1	112490897	112491073	E070	4946
chr1	112491243	112491747	E070	5292
chr1	112498538	112498669	E070	12587
chr1	112498671	112498859	E070	12720
chr1	112498867	112499005	E070	12916
chr1	112499073	112499362	E070	13122
chr1	112501279	112501355	E070	15328
chr1	112501645	112501796	E070	15694
chr1	112502229	112502283	E070	16278
chr1	112503755	112503909	E070	17804
chr1	112504005	112504170	E070	18054
chr1	112504479	112504933	E070	18528
chr1	112506418	112506504	E070	20467
chr1	112506618	112506901	E070	20667
chr1	112506910	112507040	E070	20959
chr1	112509844	112509951	E070	23893
chr1	112510040	112510222	E070	24089
chr1	112510702	112510817	E070	24751
chr1	112516149	112516286	E070	30198
chr1	112535109	112535527	E070	49158
chr1	112446520	112446577	E071	-39374
chr1	112446628	112446711	E071	-39240
chr1	112447054	112447465	E071	-38486
chr1	112447553	112447841	E071	-38110
chr1	112448053	112448114	E071	-37837
chr1	112463442	112463510	E071	-22441
chr1	112463593	112463664	E071	-22287
chr1	112464059	112464119	E071	-21832
chr1	112464605	112464835	E071	-21116
chr1	112498538	112498669	E071	12587
chr1	112498671	112498859	E071	12720
chr1	112498867	112499005	E071	12916
chr1	112499073	112499362	E071	13122
chr1	112501279	112501355	E071	15328
chr1	112501645	112501796	E071	15694
chr1	112502229	112502283	E071	16278
chr1	112502856	112502925	E071	16905
chr1	112503755	112503909	E071	17804
chr1	112504005	112504170	E071	18054
chr1	112504479	112504933	E071	18528
chr1	112506618	112506901	E071	20667
chr1	112506910	112507040	E071	20959
chr1	112507087	112507208	E071	21136
chr1	112530016	112530098	E071	44065
chr1	112445917	112445998	E072	-39953
chr1	112446520	112446577	E072	-39374
chr1	112446628	112446711	E072	-39240
chr1	112447054	112447465	E072	-38486
chr1	112447553	112447841	E072	-38110
chr1	112448053	112448114	E072	-37837
chr1	112462702	112463337	E072	-22614
chr1	112463442	112463510	E072	-22441
chr1	112463593	112463664	E072	-22287
chr1	112464059	112464119	E072	-21832
chr1	112490897	112491073	E072	4946
chr1	112501279	112501355	E072	15328
chr1	112501645	112501796	E072	15694
chr1	112503755	112503909	E072	17804
chr1	112504005	112504170	E072	18054
chr1	112504479	112504933	E072	18528
chr1	112506418	112506504	E072	20467
chr1	112506618	112506901	E072	20667
chr1	112506910	112507040	E072	20959
chr1	112507087	112507208	E072	21136
chr1	112519056	112519286	E072	33105
chr1	112535109	112535527	E072	49158
chr1	112437768	112437877	E073	-48074
chr1	112438157	112438449	E073	-47502
chr1	112446520	112446577	E073	-39374
chr1	112446628	112446711	E073	-39240
chr1	112447054	112447465	E073	-38486
chr1	112447553	112447841	E073	-38110
chr1	112448053	112448114	E073	-37837
chr1	112450076	112450213	E073	-35738
chr1	112462702	112463337	E073	-22614
chr1	112463442	112463510	E073	-22441
chr1	112463593	112463664	E073	-22287
chr1	112464059	112464119	E073	-21832
chr1	112464605	112464835	E073	-21116
chr1	112469743	112469793	E073	-16158
chr1	112472501	112472741	E073	-13210
chr1	112473048	112473243	E073	-12708
chr1	112490897	112491073	E073	4946
chr1	112491243	112491747	E073	5292
chr1	112494626	112494738	E073	8675
chr1	112501279	112501355	E073	15328
chr1	112501645	112501796	E073	15694
chr1	112502229	112502283	E073	16278
chr1	112503755	112503909	E073	17804
chr1	112504005	112504170	E073	18054
chr1	112504479	112504933	E073	18528
chr1	112506418	112506504	E073	20467
chr1	112506618	112506901	E073	20667
chr1	112506910	112507040	E073	20959
chr1	112507087	112507208	E073	21136
chr1	112523424	112523590	E073	37473
chr1	112524034	112524147	E073	38083
chr1	112535109	112535527	E073	49158
chr1	112451707	112452111	E074	-33840
chr1	112462702	112463337	E074	-22614
chr1	112463442	112463510	E074	-22441
chr1	112463593	112463664	E074	-22287
chr1	112464059	112464119	E074	-21832
chr1	112490897	112491073	E074	4946
chr1	112503755	112503909	E074	17804
chr1	112504005	112504170	E074	18054
chr1	112504479	112504933	E074	18528
chr1	112506418	112506504	E074	20467
chr1	112506618	112506901	E074	20667
chr1	112506910	112507040	E074	20959
chr1	112507087	112507208	E074	21136
chr1	112530016	112530098	E074	44065
chr1	112437768	112437877	E081	-48074
chr1	112438157	112438449	E081	-47502
chr1	112438528	112438706	E081	-47245
chr1	112445917	112445998	E081	-39953
chr1	112446520	112446577	E081	-39374
chr1	112446628	112446711	E081	-39240
chr1	112447054	112447465	E081	-38486
chr1	112447553	112447841	E081	-38110
chr1	112448053	112448114	E081	-37837
chr1	112450076	112450213	E081	-35738
chr1	112450697	112450914	E081	-35037
chr1	112451707	112452111	E081	-33840
chr1	112452297	112452404	E081	-33547
chr1	112453782	112453971	E081	-31980
chr1	112454489	112454768	E081	-31183
chr1	112454900	112455016	E081	-30935
chr1	112461379	112461478	E081	-24473
chr1	112462702	112463337	E081	-22614
chr1	112463442	112463510	E081	-22441
chr1	112463593	112463664	E081	-22287
chr1	112464059	112464119	E081	-21832
chr1	112484139	112484296	E081	-1655
chr1	112490897	112491073	E081	4946
chr1	112491243	112491747	E081	5292
chr1	112498538	112498669	E081	12587
chr1	112498671	112498859	E081	12720
chr1	112498867	112499005	E081	12916
chr1	112499073	112499362	E081	13122
chr1	112501279	112501355	E081	15328
chr1	112501645	112501796	E081	15694
chr1	112502229	112502283	E081	16278
chr1	112502856	112502925	E081	16905
chr1	112503755	112503909	E081	17804
chr1	112504005	112504170	E081	18054
chr1	112504479	112504933	E081	18528
chr1	112506418	112506504	E081	20467
chr1	112506618	112506901	E081	20667
chr1	112506910	112507040	E081	20959
chr1	112507087	112507208	E081	21136
chr1	112510702	112510817	E081	24751
chr1	112519056	112519286	E081	33105
chr1	112535109	112535527	E081	49158
chr1	112437768	112437877	E082	-48074
chr1	112438157	112438449	E082	-47502
chr1	112438528	112438706	E082	-47245
chr1	112445917	112445998	E082	-39953
chr1	112446520	112446577	E082	-39374
chr1	112446628	112446711	E082	-39240
chr1	112447054	112447465	E082	-38486
chr1	112447553	112447841	E082	-38110
chr1	112448053	112448114	E082	-37837
chr1	112449689	112449759	E082	-36192
chr1	112450076	112450213	E082	-35738
chr1	112450697	112450914	E082	-35037
chr1	112451707	112452111	E082	-33840
chr1	112452297	112452404	E082	-33547
chr1	112453782	112453971	E082	-31980
chr1	112454489	112454768	E082	-31183
chr1	112454900	112455016	E082	-30935
chr1	112463442	112463510	E082	-22441
chr1	112463593	112463664	E082	-22287
chr1	112464059	112464119	E082	-21832
chr1	112464605	112464835	E082	-21116
chr1	112484139	112484296	E082	-1655
chr1	112486464	112486547	E082	513
chr1	112486592	112486690	E082	641
chr1	112490897	112491073	E082	4946
chr1	112491243	112491747	E082	5292
chr1	112498538	112498669	E082	12587
chr1	112498671	112498859	E082	12720
chr1	112498867	112499005	E082	12916
chr1	112499073	112499362	E082	13122
chr1	112501645	112501796	E082	15694
chr1	112502229	112502283	E082	16278
chr1	112502856	112502925	E082	16905
chr1	112503755	112503909	E082	17804
chr1	112504005	112504170	E082	18054
chr1	112504479	112504933	E082	18528
chr1	112506418	112506504	E082	20467
chr1	112506618	112506901	E082	20667
chr1	112506910	112507040	E082	20959
chr1	112530016	112530098	E082	44065
chr1	112535109	112535527	E082	49158

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	112530753	112530817	E067	44802
chr1	112530985	112532007	E067	45034
chr1	112532015	112533065	E067	46064
chr1	112533199	112534400	E067	47248
chr1	112530753	112530817	E068	44802
chr1	112530985	112532007	E068	45034
chr1	112532015	112533065	E068	46064
chr1	112533199	112534400	E068	47248
chr1	112530753	112530817	E069	44802
chr1	112530985	112532007	E069	45034
chr1	112532015	112533065	E069	46064
chr1	112533199	112534400	E069	47248
chr1	112532015	112533065	E070	46064
chr1	112533199	112534400	E070	47248
chr1	112530753	112530817	E071	44802
chr1	112532015	112533065	E071	46064
chr1	112533199	112534400	E071	47248
chr1	112530753	112530817	E072	44802
chr1	112530985	112532007	E072	45034
chr1	112532015	112533065	E072	46064
chr1	112533199	112534400	E072	47248
chr1	112530753	112530817	E073	44802
chr1	112530985	112532007	E073	45034
chr1	112532015	112533065	E073	46064
chr1	112533199	112534400	E073	47248
chr1	112530985	112532007	E074	45034
chr1	112532015	112533065	E074	46064
chr1	112533199	112534400	E074	47248
chr1	112530753	112530817	E082	44802
chr1	112530985	112532007	E082	45034
chr1	112532015	112533065	E082	46064
chr1	112533199	112534400	E082	47248