rs10864468

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0081 (2439/29974,GnomAD)
A=0066 (1925/29118,TOPMED)
A=0066 (333/5008,1000G)
A=0095 (368/3854,ALSPAC)
A=0101 (376/3708,TWINSUK)

Position: chr1:10595652 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 74 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.10595652G>A
GRCh37.p13 chr 1	NC_000001.10:g.10655709G>A
PEX14 RefSeqGene	NG_008340.1:g.125707G>A

Gene: PEX14, peroxisomal biogenesis factor 14(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PEX14 transcript	NM_004565.2:c.	N/A	Intron Variant
PEX14 transcript variant X5	XM_005263470.4:c.	N/A	Intron Variant
PEX14 transcript variant X1	XM_011541577.2:c.	N/A	Intron Variant
PEX14 transcript variant X2	XM_011541578.2:c.	N/A	Intron Variant
PEX14 transcript variant X3	XM_011541579.2:c.	N/A	Intron Variant
PEX14 transcript variant X4	XM_011541580.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.991	A=0.009
1000Genomes	American	Sub	694	G=0.940	A=0.060
1000Genomes	East Asian	Sub	1008	G=0.999	A=0.001
1000Genomes	Europe	Sub	1006	G=0.882	A=0.118
1000Genomes	Global	Study-wide	5008	G=0.934	A=0.066
1000Genomes	South Asian	Sub	978	G=0.840	A=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.905	A=0.095
The Genome Aggregation Database	African	Sub	8726	G=0.981	A=0.019
The Genome Aggregation Database	American	Sub	838	G=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18488	G=0.883	A=0.116
The Genome Aggregation Database	Global	Study-wide	29974	G=0.918	A=0.081
The Genome Aggregation Database	Other	Sub	302	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.933	A=0.066
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.899	A=0.101

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
rs10864468	3.76E-06	alcohol dependence (age at onset)	24962325

eQTL of rs10864468 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 rs10864468 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	10674618	10674691	E067	18909
chr1	10676080	10676130	E067	20371
chr1	10676190	10676279	E067	20481
chr1	10619744	10619845	E068	-35864
chr1	10658122	10658519	E068	2413
chr1	10674618	10674691	E068	18909
chr1	10608343	10608589	E069	-47120
chr1	10674618	10674691	E069	18909
chr1	10676080	10676130	E069	20371
chr1	10676190	10676279	E069	20481
chr1	10639682	10639816	E070	-15893
chr1	10657285	10657517	E070	1576
chr1	10657636	10657777	E070	1927
chr1	10657802	10657902	E070	2093
chr1	10658122	10658519	E070	2413
chr1	10658521	10658674	E070	2812
chr1	10658819	10658900	E070	3110
chr1	10659286	10659975	E070	3577
chr1	10675435	10675632	E070	19726
chr1	10676080	10676130	E070	20371
chr1	10676190	10676279	E070	20481
chr1	10676383	10676433	E070	20674
chr1	10683745	10683802	E070	28036
chr1	10692059	10692263	E070	36350
chr1	10692491	10692700	E070	36782
chr1	10692869	10693116	E070	37160
chr1	10694645	10695194	E070	38936
chr1	10695242	10696319	E070	39533
chr1	10699890	10700675	E070	44181
chr1	10700718	10700866	E070	45009
chr1	10700912	10701033	E070	45203
chr1	10701085	10701135	E070	45376
chr1	10701359	10701479	E070	45650
chr1	10619540	10619590	E071	-36119
chr1	10619744	10619845	E071	-35864
chr1	10658122	10658519	E071	2413
chr1	10658521	10658674	E071	2812
chr1	10674173	10674224	E071	18464
chr1	10674618	10674691	E071	18909
chr1	10675435	10675632	E071	19726
chr1	10676080	10676130	E071	20371
chr1	10676190	10676279	E071	20481
chr1	10694645	10695194	E071	38936
chr1	10695242	10696319	E071	39533
chr1	10700718	10700866	E071	45009
chr1	10700912	10701033	E071	45203
chr1	10701085	10701135	E071	45376
chr1	10615676	10616715	E072	-38994
chr1	10619540	10619590	E072	-36119
chr1	10619744	10619845	E072	-35864
chr1	10658122	10658519	E072	2413
chr1	10674618	10674691	E072	18909
chr1	10676080	10676130	E072	20371
chr1	10676190	10676279	E072	20481
chr1	10658122	10658519	E073	2413
chr1	10694645	10695194	E073	38936
chr1	10619744	10619845	E074	-35864
chr1	10658122	10658519	E074	2413
chr1	10674618	10674691	E074	18909
chr1	10672536	10673120	E081	16827
chr1	10675435	10675632	E081	19726
chr1	10676080	10676130	E081	20371
chr1	10676190	10676279	E081	20481
chr1	10676383	10676433	E081	20674
chr1	10695242	10696319	E081	39533
chr1	10699890	10700675	E081	44181
chr1	10700718	10700866	E081	45009
chr1	10700912	10701033	E081	45203
chr1	10615552	10615650	E082	-40059
chr1	10615676	10616715	E082	-38994
chr1	10652230	10652294	E082	-3415
chr1	10675435	10675632	E082	19726
chr1	10694645	10695194	E082	38936
chr1	10695242	10696319	E082	39533

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	43104
chr1	10698970	10699106	E070	43261
chr1	10699129	10699276	E070	43420
chr1	10698304	10698417	E082	42595
chr1	10698437	10698582	E082	42728
chr1	10698617	10698657	E082	42908
chr1	10698725	10698803	E082	43016
chr1	10698813	10698918	E082	43104
chr1	10698970	10699106	E082	43261
chr1	10699129	10699276	E082	43420