rs284237

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0194 (5806/29920,GnomAD)
A=0210 (6120/29118,TOPMED)
A=0194 (970/5008,1000G)
A=0114 (441/3854,ALSPAC)
A=0123 (457/3708,TWINSUK)

Position: chr1:10618553 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 100 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.10618553G>A
GRCh37.p13 chr 1	NC_000001.10:g.10678610G>A
PEX14 RefSeqGene	NG_008340.1:g.148608G>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=0.638	A=0.362
1000Genomes	American	Sub	694	G=0.860	A=0.140
1000Genomes	East Asian	Sub	1008	G=0.942	A=0.058
1000Genomes	Europe	Sub	1006	G=0.849	A=0.151
1000Genomes	Global	Study-wide	5008	G=0.806	A=0.194
1000Genomes	South Asian	Sub	978	G=0.810	A=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.886	A=0.114
The Genome Aggregation Database	African	Sub	8702	G=0.691	A=0.309
The Genome Aggregation Database	American	Sub	838	G=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1622	G=0.910	A=0.090
The Genome Aggregation Database	Europe	Sub	18458	G=0.847	A=0.152
The Genome Aggregation Database	Global	Study-wide	29920	G=0.805	A=0.194
The Genome Aggregation Database	Other	Sub	300	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.789	A=0.210
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.877	A=0.123

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
rs284237	2.08E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284237 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 rs284237 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	-3919
chr1	10676080	10676130	E067	-2480
chr1	10676190	10676279	E067	-2331
chr1	10723387	10724295	E067	44777
chr1	10725989	10726476	E067	47379
chr1	10658122	10658519	E068	-20091
chr1	10674618	10674691	E068	-3919
chr1	10723387	10724295	E068	44777
chr1	10674618	10674691	E069	-3919
chr1	10676080	10676130	E069	-2480
chr1	10676190	10676279	E069	-2331
chr1	10723387	10724295	E069	44777
chr1	10725626	10725944	E069	47016
chr1	10725989	10726476	E069	47379
chr1	10639682	10639816	E070	-38794
chr1	10657285	10657517	E070	-21093
chr1	10657636	10657777	E070	-20833
chr1	10657802	10657902	E070	-20708
chr1	10658122	10658519	E070	-20091
chr1	10658521	10658674	E070	-19936
chr1	10658819	10658900	E070	-19710
chr1	10659286	10659975	E070	-18635
chr1	10675435	10675632	E070	-2978
chr1	10676080	10676130	E070	-2480
chr1	10676190	10676279	E070	-2331
chr1	10676383	10676433	E070	-2177
chr1	10683745	10683802	E070	5135
chr1	10692059	10692263	E070	13449
chr1	10692491	10692700	E070	13881
chr1	10692869	10693116	E070	14259
chr1	10694645	10695194	E070	16035
chr1	10695242	10696319	E070	16632
chr1	10699890	10700675	E070	21280
chr1	10700718	10700866	E070	22108
chr1	10700912	10701033	E070	22302
chr1	10701085	10701135	E070	22475
chr1	10701359	10701479	E070	22749
chr1	10708766	10708816	E070	30156
chr1	10711529	10711737	E070	32919
chr1	10711855	10712174	E070	33245
chr1	10723007	10723313	E070	44397
chr1	10723387	10724295	E070	44777
chr1	10724441	10724697	E070	45831
chr1	10658122	10658519	E071	-20091
chr1	10658521	10658674	E071	-19936
chr1	10674173	10674224	E071	-4386
chr1	10674618	10674691	E071	-3919
chr1	10675435	10675632	E071	-2978
chr1	10676080	10676130	E071	-2480
chr1	10676190	10676279	E071	-2331
chr1	10694645	10695194	E071	16035
chr1	10695242	10696319	E071	16632
chr1	10700718	10700866	E071	22108
chr1	10700912	10701033	E071	22302
chr1	10701085	10701135	E071	22475
chr1	10723007	10723313	E071	44397
chr1	10723387	10724295	E071	44777
chr1	10725626	10725944	E071	47016
chr1	10725989	10726476	E071	47379
chr1	10658122	10658519	E072	-20091
chr1	10674618	10674691	E072	-3919
chr1	10676080	10676130	E072	-2480
chr1	10676190	10676279	E072	-2331
chr1	10723007	10723313	E072	44397
chr1	10723387	10724295	E072	44777
chr1	10724441	10724697	E072	45831
chr1	10725626	10725944	E072	47016
chr1	10725989	10726476	E072	47379
chr1	10658122	10658519	E073	-20091
chr1	10694645	10695194	E073	16035
chr1	10723007	10723313	E073	44397
chr1	10723387	10724295	E073	44777
chr1	10658122	10658519	E074	-20091
chr1	10674618	10674691	E074	-3919
chr1	10723387	10724295	E074	44777
chr1	10725626	10725944	E074	47016
chr1	10725989	10726476	E074	47379
chr1	10726487	10726755	E074	47877
chr1	10672536	10673120	E081	-5490
chr1	10675435	10675632	E081	-2978
chr1	10676080	10676130	E081	-2480
chr1	10676190	10676279	E081	-2331
chr1	10676383	10676433	E081	-2177
chr1	10695242	10696319	E081	16632
chr1	10699890	10700675	E081	21280
chr1	10700718	10700866	E081	22108
chr1	10700912	10701033	E081	22302
chr1	10711529	10711737	E081	32919
chr1	10711855	10712174	E081	33245
chr1	10722583	10722820	E081	43973
chr1	10722892	10722989	E081	44282
chr1	10723007	10723313	E081	44397
chr1	10723387	10724295	E081	44777
chr1	10724441	10724697	E081	45831
chr1	10652230	10652294	E082	-26316
chr1	10675435	10675632	E082	-2978
chr1	10694645	10695194	E082	16035
chr1	10695242	10696319	E082	16632
chr1	10723387	10724295	E082	44777
chr1	10724441	10724697	E082	45831

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	20203
chr1	10698970	10699106	E070	20360
chr1	10699129	10699276	E070	20519
chr1	10698304	10698417	E082	19694
chr1	10698437	10698582	E082	19827
chr1	10698617	10698657	E082	20007
chr1	10698725	10698803	E082	20115
chr1	10698813	10698918	E082	20203
chr1	10698970	10699106	E082	20360
chr1	10699129	10699276	E082	20519