rs1896857

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ANKRD44 : Intron Variant
ANKRD44-IT1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0377 (11296/29914,GnomAD)
G=0336 (9793/29118,TOPMED)
G=0365 (1829/5008,1000G)
G=0344 (1326/3854,ALSPAC)
G=0342 (1269/3708,TWINSUK)

Position: chr2:197299806 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 213 Enhancers around

Promoter: 15 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.197299806A>G
GRCh37.p13 chr 2	NC_000002.11:g.198164530A>G

Gene: ANKRD44, ankyrin repeat domain 44(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANKRD44 transcript variant A	NM_001195144.1:c.	N/A	Intron Variant
ANKRD44 transcript variant B	NM_153697.2:c.	N/A	Intron Variant
ANKRD44 transcript variant X1	XM_005246945.1:c.	N/A	Intron Variant
ANKRD44 transcript variant X2	XM_005246946.1:c.	N/A	Intron Variant
ANKRD44 transcript variant X4	XM_005246947.2:c.	N/A	Intron Variant
ANKRD44 transcript variant X7	XM_005246948.2:c.	N/A	Intron Variant
ANKRD44 transcript variant X6	XM_006712838.3:c.	N/A	Intron Variant
ANKRD44 transcript variant X5	XM_011512148.2:c.	N/A	Intron Variant
ANKRD44 transcript variant X9	XM_017005252.1:c.	N/A	Intron Variant
ANKRD44 transcript variant X8	XR_001739037.1:n.	N/A	Intron Variant
ANKRD44 transcript variant X11	XR_001739038.1:n.	N/A	Intron Variant
ANKRD44 transcript variant X10	XR_923062.2:n.	N/A	Intron Variant

Gene: ANKRD44-IT1, ANKRD44 intronic transcript 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANKRD44-IT1 transcript	NR_046837.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.698	G=0.302
1000Genomes	American	Sub	694	A=0.590	G=0.410
1000Genomes	East Asian	Sub	1008	A=0.500	G=0.500
1000Genomes	Europe	Sub	1006	A=0.706	G=0.294
1000Genomes	Global	Study-wide	5008	A=0.635	G=0.365
1000Genomes	South Asian	Sub	978	A=0.650	G=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.656	G=0.344
The Genome Aggregation Database	African	Sub	8704	A=0.678	G=0.322
The Genome Aggregation Database	American	Sub	834	A=0.510	G=0.490
The Genome Aggregation Database	East Asian	Sub	1620	A=0.496	G=0.504
The Genome Aggregation Database	Europe	Sub	18454	A=0.610	G=0.389
The Genome Aggregation Database	Global	Study-wide	29914	A=0.622	G=0.377
The Genome Aggregation Database	Other	Sub	302	A=0.710	G=0.290
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.663	G=0.336
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.658	G=0.342

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
rs1896857	8E-06	alcohol dependence (age at onset)	24962325

eQTL of rs1896857 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198164530	SF3B1	ENSG00000115524.11	A>G	7.6222e-4	-135285	Caudate_basal_ganglia

meQTL of rs1896857 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	198119577	198121990	E067	-42540
chr2	198132614	198132691	E067	-31839
chr2	198132933	198132981	E067	-31549
chr2	198134034	198134260	E067	-30270
chr2	198134572	198134822	E067	-29708
chr2	198135093	198135452	E067	-29078
chr2	198135680	198135771	E067	-28759
chr2	198144187	198144302	E067	-20228
chr2	198144797	198144963	E067	-19567
chr2	198144991	198145439	E067	-19091
chr2	198148952	198149064	E067	-15466
chr2	198149164	198149370	E067	-15160
chr2	198151792	198151914	E067	-12616
chr2	198170850	198171284	E067	6320
chr2	198171319	198171761	E067	6789
chr2	198114561	198114624	E068	-49906
chr2	198114827	198114968	E068	-49562
chr2	198119373	198119465	E068	-45065
chr2	198119577	198121990	E068	-42540
chr2	198133447	198133498	E068	-31032
chr2	198133864	198133982	E068	-30548
chr2	198134034	198134260	E068	-30270
chr2	198134572	198134822	E068	-29708
chr2	198135093	198135452	E068	-29078
chr2	198138103	198138275	E068	-26255
chr2	198138299	198138559	E068	-25971
chr2	198138758	198138855	E068	-25675
chr2	198144187	198144302	E068	-20228
chr2	198149847	198149931	E068	-14599
chr2	198150055	198150273	E068	-14257
chr2	198150290	198150431	E068	-14099
chr2	198150666	198150730	E068	-13800
chr2	198150906	198151063	E068	-13467
chr2	198151792	198151914	E068	-12616
chr2	198152060	198152409	E068	-12121
chr2	198157345	198157716	E068	-6814
chr2	198159594	198159711	E068	-4819
chr2	198159963	198160038	E068	-4492
chr2	198167276	198167357	E068	2746
chr2	198167399	198167439	E068	2869
chr2	198170850	198171284	E068	6320
chr2	198171319	198171761	E068	6789
chr2	198119577	198121990	E069	-42540
chr2	198133447	198133498	E069	-31032
chr2	198133864	198133982	E069	-30548
chr2	198134034	198134260	E069	-30270
chr2	198134572	198134822	E069	-29708
chr2	198135093	198135452	E069	-29078
chr2	198138103	198138275	E069	-26255
chr2	198138299	198138559	E069	-25971
chr2	198142779	198142861	E069	-21669
chr2	198143460	198143851	E069	-20679
chr2	198143856	198143916	E069	-20614
chr2	198144187	198144302	E069	-20228
chr2	198144797	198144963	E069	-19567
chr2	198144991	198145439	E069	-19091
chr2	198148952	198149064	E069	-15466
chr2	198149164	198149370	E069	-15160
chr2	198149847	198149931	E069	-14599
chr2	198150055	198150273	E069	-14257
chr2	198150290	198150431	E069	-14099
chr2	198151792	198151914	E069	-12616
chr2	198152060	198152409	E069	-12121
chr2	198157345	198157716	E069	-6814
chr2	198166925	198167174	E069	2395
chr2	198167276	198167357	E069	2746
chr2	198167399	198167439	E069	2869
chr2	198170850	198171284	E069	6320
chr2	198171319	198171761	E069	6789
chr2	198119577	198121990	E070	-42540
chr2	198134572	198134822	E070	-29708
chr2	198142013	198142166	E070	-22364
chr2	198142779	198142861	E070	-21669
chr2	198119373	198119465	E071	-45065
chr2	198119577	198121990	E071	-42540
chr2	198126342	198127138	E071	-37392
chr2	198132298	198132359	E071	-32171
chr2	198132614	198132691	E071	-31839
chr2	198132933	198132981	E071	-31549
chr2	198133447	198133498	E071	-31032
chr2	198133864	198133982	E071	-30548
chr2	198134034	198134260	E071	-30270
chr2	198134572	198134822	E071	-29708
chr2	198135093	198135452	E071	-29078
chr2	198138103	198138275	E071	-26255
chr2	198138299	198138559	E071	-25971
chr2	198138758	198138855	E071	-25675
chr2	198139212	198139351	E071	-25179
chr2	198142013	198142166	E071	-22364
chr2	198142779	198142861	E071	-21669
chr2	198143460	198143851	E071	-20679
chr2	198143856	198143916	E071	-20614
chr2	198144187	198144302	E071	-20228
chr2	198144797	198144963	E071	-19567
chr2	198144991	198145439	E071	-19091
chr2	198145472	198145598	E071	-18932
chr2	198150055	198150273	E071	-14257
chr2	198150290	198150431	E071	-14099
chr2	198150666	198150730	E071	-13800
chr2	198151792	198151914	E071	-12616
chr2	198152060	198152409	E071	-12121
chr2	198157345	198157716	E071	-6814
chr2	198159594	198159711	E071	-4819
chr2	198166925	198167174	E071	2395
chr2	198167276	198167357	E071	2746
chr2	198167399	198167439	E071	2869
chr2	198170850	198171284	E071	6320
chr2	198171319	198171761	E071	6789
chr2	198119577	198121990	E072	-42540
chr2	198132298	198132359	E072	-32171
chr2	198132614	198132691	E072	-31839
chr2	198132933	198132981	E072	-31549
chr2	198133447	198133498	E072	-31032
chr2	198133864	198133982	E072	-30548
chr2	198134034	198134260	E072	-30270
chr2	198134572	198134822	E072	-29708
chr2	198135093	198135452	E072	-29078
chr2	198135680	198135771	E072	-28759
chr2	198138103	198138275	E072	-26255
chr2	198138299	198138559	E072	-25971
chr2	198138758	198138855	E072	-25675
chr2	198139212	198139351	E072	-25179
chr2	198143460	198143851	E072	-20679
chr2	198143856	198143916	E072	-20614
chr2	198144187	198144302	E072	-20228
chr2	198144797	198144963	E072	-19567
chr2	198148952	198149064	E072	-15466
chr2	198149847	198149931	E072	-14599
chr2	198150055	198150273	E072	-14257
chr2	198150290	198150431	E072	-14099
chr2	198150666	198150730	E072	-13800
chr2	198151792	198151914	E072	-12616
chr2	198152060	198152409	E072	-12121
chr2	198167276	198167357	E072	2746
chr2	198170850	198171284	E072	6320
chr2	198171319	198171761	E072	6789
chr2	198133864	198133982	E073	-30548
chr2	198134034	198134260	E073	-30270
chr2	198134572	198134822	E073	-29708
chr2	198144187	198144302	E073	-20228
chr2	198151792	198151914	E073	-12616
chr2	198170850	198171284	E073	6320
chr2	198171319	198171761	E073	6789
chr2	198119577	198121990	E074	-42540
chr2	198126342	198127138	E074	-37392
chr2	198127140	198127264	E074	-37266
chr2	198130749	198130902	E074	-33628
chr2	198130978	198131490	E074	-33040
chr2	198132933	198132981	E074	-31549
chr2	198133447	198133498	E074	-31032
chr2	198133864	198133982	E074	-30548
chr2	198134034	198134260	E074	-30270
chr2	198134572	198134822	E074	-29708
chr2	198135093	198135452	E074	-29078
chr2	198138103	198138275	E074	-26255
chr2	198138299	198138559	E074	-25971
chr2	198144187	198144302	E074	-20228
chr2	198144797	198144963	E074	-19567
chr2	198144991	198145439	E074	-19091
chr2	198145472	198145598	E074	-18932
chr2	198149164	198149370	E074	-15160
chr2	198149847	198149931	E074	-14599
chr2	198150055	198150273	E074	-14257
chr2	198150290	198150431	E074	-14099
chr2	198150666	198150730	E074	-13800
chr2	198151792	198151914	E074	-12616
chr2	198152060	198152409	E074	-12121
chr2	198157345	198157716	E074	-6814
chr2	198159594	198159711	E074	-4819
chr2	198159963	198160038	E074	-4492
chr2	198167399	198167439	E074	2869
chr2	198170850	198171284	E074	6320
chr2	198171319	198171761	E074	6789
chr2	198119373	198119465	E081	-45065
chr2	198119577	198121990	E081	-42540
chr2	198129138	198129394	E081	-35136
chr2	198132298	198132359	E081	-32171
chr2	198132614	198132691	E081	-31839
chr2	198132933	198132981	E081	-31549
chr2	198133447	198133498	E081	-31032
chr2	198133864	198133982	E081	-30548
chr2	198134034	198134260	E081	-30270
chr2	198134572	198134822	E081	-29708
chr2	198135093	198135452	E081	-29078
chr2	198138103	198138275	E081	-26255
chr2	198138299	198138559	E081	-25971
chr2	198138758	198138855	E081	-25675
chr2	198139212	198139351	E081	-25179
chr2	198150055	198150273	E081	-14257
chr2	198150666	198150730	E081	-13800
chr2	198170850	198171284	E081	6320
chr2	198171319	198171761	E081	6789
chr2	198192009	198192838	E081	27479
chr2	198192906	198192981	E081	28376
chr2	198193177	198193238	E081	28647
chr2	198204888	198205006	E081	40358
chr2	198205438	198206161	E081	40908
chr2	198208450	198208504	E081	43920
chr2	198208741	198208947	E081	44211
chr2	198119577	198121990	E082	-42540
chr2	198124018	198124076	E082	-40454
chr2	198124115	198124231	E082	-40299
chr2	198124356	198124450	E082	-40080
chr2	198126342	198127138	E082	-37392
chr2	198127140	198127264	E082	-37266
chr2	198134572	198134822	E082	-29708
chr2	198135093	198135452	E082	-29078
chr2	198135680	198135771	E082	-28759
chr2	198138103	198138275	E082	-26255
chr2	198138299	198138559	E082	-25971
chr2	198170850	198171284	E082	6320
chr2	198192906	198192981	E082	28376
chr2	198193177	198193238	E082	28647

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	198173339	198173697	E067	8809
chr2	198173785	198176822	E067	9255
chr2	198173339	198173697	E068	8809
chr2	198173785	198176822	E068	9255
chr2	198173339	198173697	E069	8809
chr2	198173785	198176822	E069	9255
chr2	198173785	198176822	E070	9255
chr2	198173339	198173697	E071	8809
chr2	198173785	198176822	E071	9255
chr2	198173785	198176822	E072	9255
chr2	198173785	198176822	E073	9255
chr2	198173785	198176822	E074	9255
chr2	198173785	198176822	E081	9255
chr2	198173339	198173697	E082	8809
chr2	198173785	198176822	E082	9255