rs13374159

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ACP6 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0064 (1931/29950,GnomAD)
T=0096 (2814/29118,TOPMED)
T=0077 (384/5008,1000G)
T=0008 (31/3854,ALSPAC)
T=0010 (38/3708,TWINSUK)

Position: chr1:147670335 (GRCh38.p7) (1q21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 68 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.147670335C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.4485748C>T
GRCh37.p13 chr 1	NC_000001.10:g.147142457C>T

Gene: ACP6, acid phosphatase 6, lysophosphatidic(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ACP6 transcript variant 1	NM_016361.4:c.	N/A	5 Prime UTR Variant
ACP6 transcript variant 2	NM_001323625.1:c.	N/A	5 Prime UTR Variant
ACP6 transcript variant 4	NR_136634.1:n.209G>A	G>A	Non Coding Transcript Variant
ACP6 transcript variant 3	NR_136633.1:n.209G>A	G>A	Non Coding Transcript Variant
ACP6 transcript variant 6	NR_136636.1:n.209G>A	G>A	Non Coding Transcript Variant
ACP6 transcript variant 5	NR_136635.1:n.209G>A	G>A	Non Coding Transcript Variant
ACP6 transcript variant X1	XM_011509601.2:c.	N/A	5 Prime UTR Variant
ACP6 transcript variant X2	XM_017001422.1:c.	N/A	5 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.754	T=0.246
1000Genomes	American	Sub	694	C=0.980	T=0.020
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=0.997	T=0.003
1000Genomes	Global	Study-wide	5008	C=0.923	T=0.077
1000Genomes	South Asian	Sub	978	C=0.960	T=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.992	T=0.008
The Genome Aggregation Database	African	Sub	8708	C=0.796	T=0.204
The Genome Aggregation Database	American	Sub	838	C=0.980	T=0.020
The Genome Aggregation Database	East Asian	Sub	1622	C=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18480	C=0.992	T=0.007
The Genome Aggregation Database	Global	Study-wide	29950	C=0.935	T=0.064
The Genome Aggregation Database	Other	Sub	302	C=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.903	T=0.096
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.990	T=0.010

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
rs13374159	0.000626	alcohol dependence	20201924

eQTL of rs13374159 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 rs13374159 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	4456663	4456887	E067	-28861
chr1	4457375	4457590	E067	-28158
chr1	4490888	4491503	E067	5140
chr1	4491586	4491928	E067	5838
chr1	4528988	4529124	E067	43240
chr1	4456663	4456887	E068	-28861
chr1	4457375	4457590	E068	-28158
chr1	4457638	4457728	E068	-28020
chr1	4458229	4458559	E068	-27189
chr1	4455902	4455968	E069	-29780
chr1	4456663	4456887	E069	-28861
chr1	4457375	4457590	E069	-28158
chr1	4457638	4457728	E069	-28020
chr1	4455302	4455472	E070	-30276
chr1	4455902	4455968	E070	-29780
chr1	4456663	4456887	E070	-28861
chr1	4457375	4457590	E070	-28158
chr1	4457638	4457728	E070	-28020
chr1	4458229	4458559	E070	-27189
chr1	4481369	4481445	E070	-4303
chr1	4481548	4481670	E070	-4078
chr1	4482669	4482872	E070	-2876
chr1	4507985	4508077	E070	22237
chr1	4508185	4508417	E070	22437
chr1	4510486	4510541	E070	24738
chr1	4456663	4456887	E071	-28861
chr1	4457638	4457728	E071	-28020
chr1	4458229	4458559	E071	-27189
chr1	4507985	4508077	E071	22237
chr1	4456663	4456887	E072	-28861
chr1	4457375	4457590	E072	-28158
chr1	4457638	4457728	E072	-28020
chr1	4458229	4458559	E072	-27189
chr1	4528988	4529124	E072	43240
chr1	4455302	4455472	E073	-30276
chr1	4455902	4455968	E073	-29780
chr1	4456663	4456887	E073	-28861
chr1	4457375	4457590	E073	-28158
chr1	4481548	4481670	E073	-4078
chr1	4482669	4482872	E073	-2876
chr1	4490888	4491503	E073	5140
chr1	4491586	4491928	E073	5838
chr1	4455902	4455968	E074	-29780
chr1	4456663	4456887	E074	-28861
chr1	4457375	4457590	E074	-28158
chr1	4457638	4457728	E074	-28020
chr1	4458229	4458559	E074	-27189
chr1	4456663	4456887	E081	-28861
chr1	4457375	4457590	E081	-28158
chr1	4457638	4457728	E081	-28020
chr1	4458229	4458559	E081	-27189
chr1	4481369	4481445	E081	-4303
chr1	4481548	4481670	E081	-4078
chr1	4482669	4482872	E081	-2876
chr1	4490888	4491503	E081	5140
chr1	4491586	4491928	E081	5838
chr1	4492449	4492640	E081	6701
chr1	4512760	4512908	E081	27012
chr1	4512964	4513166	E081	27216
chr1	4456663	4456887	E082	-28861
chr1	4457375	4457590	E082	-28158
chr1	4457638	4457728	E082	-28020
chr1	4458229	4458559	E082	-27189
chr1	4481369	4481445	E082	-4303
chr1	4481548	4481670	E082	-4078
chr1	4482669	4482872	E082	-2876
chr1	4507985	4508077	E082	22237
chr1	4508185	4508417	E082	22437