rs12722934

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0337 (10107/29930,GnomAD)
A==0366 (10667/29118,TOPMED)
A==0404 (2025/5008,1000G)
A==0206 (795/3854,ALSPAC)
A==0215 (798/3708,TWINSUK)

Position: chr1:10608322 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 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.10608322A>T
GRCh37.p13 chr 1	NC_000001.10:g.10668379A>T
PEX14 RefSeqGene	NG_008340.1:g.138377A>T

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	A=0.641	T=0.359
1000Genomes	American	Sub	694	A=0.220	T=0.780
1000Genomes	East Asian	Sub	1008	A=0.424	T=0.576
1000Genomes	Europe	Sub	1006	A=0.217	T=0.783
1000Genomes	Global	Study-wide	5008	A=0.404	T=0.596
1000Genomes	South Asian	Sub	978	A=0.390	T=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.206	T=0.794
The Genome Aggregation Database	African	Sub	8690	A=0.556	T=0.444
The Genome Aggregation Database	American	Sub	838	A=0.190	T=0.810
The Genome Aggregation Database	East Asian	Sub	1614	A=0.442	T=0.558
The Genome Aggregation Database	Europe	Sub	18486	A=0.234	T=0.765
The Genome Aggregation Database	Global	Study-wide	29930	A=0.337	T=0.662
The Genome Aggregation Database	Other	Sub	302	A=0.250	T=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.366	T=0.633
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.215	T=0.785

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
rs12722934	3.08E-06	alcohol dependence (age at onset)	24962325

eQTL of rs12722934 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 rs12722934 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg14427972	chr9:140771180	CACNA1B	-0.0311963607344189	8.5952e-9

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	6239
chr1	10676080	10676130	E067	7701
chr1	10676190	10676279	E067	7811
chr1	10619744	10619845	E068	-48534
chr1	10658122	10658519	E068	-9860
chr1	10674618	10674691	E068	6239
chr1	10674618	10674691	E069	6239
chr1	10676080	10676130	E069	7701
chr1	10676190	10676279	E069	7811
chr1	10639682	10639816	E070	-28563
chr1	10657285	10657517	E070	-10862
chr1	10657636	10657777	E070	-10602
chr1	10657802	10657902	E070	-10477
chr1	10658122	10658519	E070	-9860
chr1	10658521	10658674	E070	-9705
chr1	10658819	10658900	E070	-9479
chr1	10659286	10659975	E070	-8404
chr1	10675435	10675632	E070	7056
chr1	10676080	10676130	E070	7701
chr1	10676190	10676279	E070	7811
chr1	10676383	10676433	E070	8004
chr1	10683745	10683802	E070	15366
chr1	10692059	10692263	E070	23680
chr1	10692491	10692700	E070	24112
chr1	10692869	10693116	E070	24490
chr1	10694645	10695194	E070	26266
chr1	10695242	10696319	E070	26863
chr1	10699890	10700675	E070	31511
chr1	10700718	10700866	E070	32339
chr1	10700912	10701033	E070	32533
chr1	10701085	10701135	E070	32706
chr1	10701359	10701479	E070	32980
chr1	10708766	10708816	E070	40387
chr1	10711529	10711737	E070	43150
chr1	10711855	10712174	E070	43476
chr1	10619540	10619590	E071	-48789
chr1	10619744	10619845	E071	-48534
chr1	10658122	10658519	E071	-9860
chr1	10658521	10658674	E071	-9705
chr1	10674173	10674224	E071	5794
chr1	10674618	10674691	E071	6239
chr1	10675435	10675632	E071	7056
chr1	10676080	10676130	E071	7701
chr1	10676190	10676279	E071	7811
chr1	10694645	10695194	E071	26266
chr1	10695242	10696319	E071	26863
chr1	10700718	10700866	E071	32339
chr1	10700912	10701033	E071	32533
chr1	10701085	10701135	E071	32706
chr1	10619540	10619590	E072	-48789
chr1	10619744	10619845	E072	-48534
chr1	10658122	10658519	E072	-9860
chr1	10674618	10674691	E072	6239
chr1	10676080	10676130	E072	7701
chr1	10676190	10676279	E072	7811
chr1	10658122	10658519	E073	-9860
chr1	10694645	10695194	E073	26266
chr1	10619744	10619845	E074	-48534
chr1	10658122	10658519	E074	-9860
chr1	10674618	10674691	E074	6239
chr1	10672536	10673120	E081	4157
chr1	10675435	10675632	E081	7056
chr1	10676080	10676130	E081	7701
chr1	10676190	10676279	E081	7811
chr1	10676383	10676433	E081	8004
chr1	10695242	10696319	E081	26863
chr1	10699890	10700675	E081	31511
chr1	10700718	10700866	E081	32339
chr1	10700912	10701033	E081	32533
chr1	10711529	10711737	E081	43150
chr1	10711855	10712174	E081	43476
chr1	10652230	10652294	E082	-16085
chr1	10675435	10675632	E082	7056
chr1	10694645	10695194	E082	26266
chr1	10695242	10696319	E082	26863

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	30434
chr1	10698970	10699106	E070	30591
chr1	10699129	10699276	E070	30750
chr1	10698304	10698417	E082	29925
chr1	10698437	10698582	E082	30058
chr1	10698617	10698657	E082	30238
chr1	10698725	10698803	E082	30346
chr1	10698813	10698918	E082	30434
chr1	10698970	10699106	E082	30591
chr1	10699129	10699276	E082	30750