rs17126643

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

CACHD1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0115 (3461/29922,GnomAD)
G=0167 (4870/29118,TOPMED)
G=0111 (554/5008,1000G)
G=0044 (171/3854,ALSPAC)
G=0050 (185/3708,TWINSUK)

Position: chr1:64544923 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 151 Enhancers around

Promoter: 7 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.64544923T>G
GRCh37.p13 chr 1	NC_000001.10:g.65010606T>G

Gene: CACHD1, cache domain containing 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACHD1 transcript variant 2	NM_001293274.1:c.	N/A	Intron Variant
CACHD1 transcript variant 1	NM_020925.2:c.	N/A	Intron Variant
CACHD1 transcript variant X1	XM_011541862.1:c.	N/A	Intron Variant
CACHD1 transcript variant X2	XM_011541863.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.660	G=0.340
1000Genomes	American	Sub	694	T=0.940	G=0.060
1000Genomes	East Asian	Sub	1008	T=0.998	G=0.002
1000Genomes	Europe	Sub	1006	T=0.951	G=0.049
1000Genomes	Global	Study-wide	5008	T=0.889	G=0.111
1000Genomes	South Asian	Sub	978	T=0.990	G=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.956	G=0.044
The Genome Aggregation Database	African	Sub	8682	T=0.689	G=0.311
The Genome Aggregation Database	American	Sub	836	T=0.950	G=0.050
The Genome Aggregation Database	East Asian	Sub	1622	T=0.999	G=0.001
The Genome Aggregation Database	Europe	Sub	18480	T=0.961	G=0.038
The Genome Aggregation Database	Global	Study-wide	29922	T=0.884	G=0.115
The Genome Aggregation Database	Other	Sub	302	T=0.970	G=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.832	G=0.167
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.950	G=0.050

PMID	Title	Author	Journal
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs17126643	6.43E-05	alcohol consumption	23953852

eQTL of rs17126643 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 rs17126643 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	64969462	64969561	E067	-41045
chr1	64978073	64978303	E067	-32303
chr1	65006865	65006947	E067	-3659
chr1	64962940	64963060	E068	-47546
chr1	64963209	64963533	E068	-47073
chr1	64963777	64963882	E068	-46724
chr1	64967996	64968293	E068	-42313
chr1	64968524	64968646	E068	-41960
chr1	64970442	64970497	E068	-40109
chr1	64970531	64970611	E068	-39995
chr1	64970687	64970741	E068	-39865
chr1	64976859	64977032	E068	-33574
chr1	64977262	64977311	E068	-33295
chr1	64977392	64977456	E068	-33150
chr1	64978073	64978303	E068	-32303
chr1	64978333	64978392	E068	-32214
chr1	64978551	64978715	E068	-31891
chr1	64979110	64979160	E068	-31446
chr1	64979398	64979510	E068	-31096
chr1	64979559	64980482	E068	-30124
chr1	64980688	64980741	E068	-29865
chr1	64980983	64981067	E068	-29539
chr1	64981087	64981454	E068	-29152
chr1	64982043	64982228	E068	-28378
chr1	64982590	64982748	E068	-27858
chr1	64982897	64983066	E068	-27540
chr1	64989180	64989368	E068	-21238
chr1	64989484	64989528	E068	-21078
chr1	64989753	64989853	E068	-20753
chr1	64990879	64990997	E068	-19609
chr1	64991373	64991423	E068	-19183
chr1	64991548	64991625	E068	-18981
chr1	64992428	64992526	E068	-18080
chr1	64992547	64992750	E068	-17856
chr1	64992835	64992919	E068	-17687
chr1	64992941	64993241	E068	-17365
chr1	64993506	64993727	E068	-16879
chr1	64996659	64996994	E068	-13612
chr1	64997421	64997500	E068	-13106
chr1	65002836	65003178	E068	-7428
chr1	65004657	65004938	E068	-5668
chr1	65006865	65006947	E068	-3659
chr1	65010928	65011351	E068	322
chr1	65011463	65011550	E068	857
chr1	65037957	65038508	E068	27351
chr1	65042175	65042269	E068	31569
chr1	65059984	65060028	E068	49378
chr1	65060030	65060087	E068	49424
chr1	65060145	65060388	E068	49539
chr1	65060438	65060482	E068	49832
chr1	64978551	64978715	E069	-31891
chr1	64979110	64979160	E069	-31446
chr1	64982043	64982228	E069	-28378
chr1	65006865	65006947	E069	-3659
chr1	64967717	64967971	E070	-42635
chr1	64967996	64968293	E070	-42313
chr1	64968524	64968646	E070	-41960
chr1	64968684	64969036	E070	-41570
chr1	64969059	64969262	E070	-41344
chr1	64969305	64969360	E070	-41246
chr1	64969462	64969561	E070	-41045
chr1	64974366	64974539	E070	-36067
chr1	64974541	64974700	E070	-35906
chr1	64974814	64974864	E070	-35742
chr1	64980983	64981067	E070	-29539
chr1	64981087	64981454	E070	-29152
chr1	65004657	65004938	E070	-5668
chr1	65006865	65006947	E070	-3659
chr1	65054622	65054898	E070	44016
chr1	64962940	64963060	E071	-47546
chr1	64963209	64963533	E071	-47073
chr1	64976144	64976204	E071	-34402
chr1	64979110	64979160	E071	-31446
chr1	64979398	64979510	E071	-31096
chr1	64979559	64980482	E071	-30124
chr1	64980688	64980741	E071	-29865
chr1	64980983	64981067	E071	-29539
chr1	64981087	64981454	E071	-29152
chr1	64982043	64982228	E071	-28378
chr1	64982590	64982748	E071	-27858
chr1	64982897	64983066	E071	-27540
chr1	65004657	65004938	E071	-5668
chr1	65042175	65042269	E071	31569
chr1	65047249	65047328	E071	36643
chr1	65047345	65047459	E071	36739
chr1	65047610	65047708	E071	37004
chr1	64970442	64970497	E072	-40109
chr1	64970531	64970611	E072	-39995
chr1	64970687	64970741	E072	-39865
chr1	64972823	64973106	E072	-37500
chr1	64973156	64973357	E072	-37249
chr1	64978073	64978303	E072	-32303
chr1	64978333	64978392	E072	-32214
chr1	64978551	64978715	E072	-31891
chr1	64979110	64979160	E072	-31446
chr1	64979398	64979510	E072	-31096
chr1	64979559	64980482	E072	-30124
chr1	64980688	64980741	E072	-29865
chr1	64970442	64970497	E073	-40109
chr1	64977392	64977456	E073	-33150
chr1	64978073	64978303	E073	-32303
chr1	64978333	64978392	E073	-32214
chr1	64978551	64978715	E073	-31891
chr1	64979110	64979160	E073	-31446
chr1	64979398	64979510	E073	-31096
chr1	64979559	64980482	E073	-30124
chr1	64981087	64981454	E073	-29152
chr1	64982043	64982228	E073	-28378
chr1	65001939	65002436	E073	-8170
chr1	65006865	65006947	E073	-3659
chr1	65009961	65010283	E073	-323
chr1	64969305	64969360	E074	-41246
chr1	64970442	64970497	E074	-40109
chr1	64970531	64970611	E074	-39995
chr1	64970687	64970741	E074	-39865
chr1	64978073	64978303	E074	-32303
chr1	64978333	64978392	E074	-32214
chr1	64978551	64978715	E074	-31891
chr1	64982043	64982228	E074	-28378
chr1	65006865	65006947	E074	-3659
chr1	65047249	65047328	E074	36643
chr1	65047345	65047459	E074	36739
chr1	64970442	64970497	E081	-40109
chr1	64970531	64970611	E081	-39995
chr1	64970687	64970741	E081	-39865
chr1	64972823	64973106	E081	-37500
chr1	64973156	64973357	E081	-37249
chr1	64974366	64974539	E081	-36067
chr1	64974541	64974700	E081	-35906
chr1	64974814	64974864	E081	-35742
chr1	64979398	64979510	E081	-31096
chr1	64979559	64980482	E081	-30124
chr1	64980688	64980741	E081	-29865
chr1	64980983	64981067	E081	-29539
chr1	64981087	64981454	E081	-29152
chr1	64993506	64993727	E081	-16879
chr1	65005027	65006747	E081	-3859
chr1	65006865	65006947	E081	-3659
chr1	64972823	64973106	E082	-37500
chr1	64973156	64973357	E082	-37249
chr1	64974366	64974539	E082	-36067
chr1	64974541	64974700	E082	-35906
chr1	64974814	64974864	E082	-35742
chr1	64979110	64979160	E082	-31446
chr1	64979559	64980482	E082	-30124
chr1	64980688	64980741	E082	-29865
chr1	64980983	64981067	E082	-29539
chr1	64981087	64981454	E082	-29152
chr1	64982043	64982228	E082	-28378
chr1	64982897	64983066	E082	-27540
chr1	65005027	65006747	E082	-3859

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	64970840	64972482	E067	-38124
chr1	64970840	64972482	E068	-38124
chr1	64970840	64972482	E069	-38124
chr1	64970840	64972482	E070	-38124
chr1	64970840	64972482	E072	-38124
chr1	64970840	64972482	E073	-38124
chr1	64970840	64972482	E082	-38124