rs284238

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0157 (18994/120314,ExAC)
T=0195 (5844/29952,GnomAD)
T=0211 (6144/29118,TOPMED)
A==0186 (2426/13006,GO-ESP)
T=0195 (976/5008,1000G)
T=0114 (440/3854,ALSPAC)
T=0123 (457/3708,TWINSUK)

Position: chr1:10618431 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 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.10618431A>T
GRCh37.p13 chr 1	NC_000001.10:g.10678488A>T
PEX14 RefSeqGene	NG_008340.1:g.148486A>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=0.634	T=0.366
1000Genomes	American	Sub	694	A=0.860	T=0.140
1000Genomes	East Asian	Sub	1008	A=0.941	T=0.059
1000Genomes	Europe	Sub	1006	A=0.850	T=0.150
1000Genomes	Global	Study-wide	5008	A=0.805	T=0.195
1000Genomes	South Asian	Sub	978	A=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.886	T=0.114
The Exome Aggregation Consortium	American	Sub	21774	A=0.802	T=0.197
The Exome Aggregation Consortium	Asian	Sub	25028	A=0.838	T=0.161
The Exome Aggregation Consortium	Europe	Sub	72630	A=0.855	T=0.144
The Exome Aggregation Consortium	Global	Study-wide	120314	A=0.842	T=0.157
The Exome Aggregation Consortium	Other	Sub	882	A=0.800	T=0.200
The Genome Aggregation Database	African	Sub	8728	A=0.690	T=0.310
The Genome Aggregation Database	American	Sub	836	A=0.880	T=0.120
The Genome Aggregation Database	East Asian	Sub	1620	A=0.909	T=0.091
The Genome Aggregation Database	Europe	Sub	18468	A=0.846	T=0.153
The Genome Aggregation Database	Global	Study-wide	29952	A=0.804	T=0.195
The Genome Aggregation Database	Other	Sub	300	A=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.789	T=0.211
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.877	T=0.123

PMID	Title	Author	Journal
23757202	Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.	Bean LJ	Hum Mutat
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S	Genet Med

P-Value

SNP ID	p-value	Traits	Study
rs284238	1.61E-06	alcohol dependence (age at onset)	24962325

eQTL of rs284238 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 rs284238 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	-3797
chr1	10676080	10676130	E067	-2358
chr1	10676190	10676279	E067	-2209
chr1	10723387	10724295	E067	44899
chr1	10725989	10726476	E067	47501
chr1	10658122	10658519	E068	-19969
chr1	10674618	10674691	E068	-3797
chr1	10723387	10724295	E068	44899
chr1	10674618	10674691	E069	-3797
chr1	10676080	10676130	E069	-2358
chr1	10676190	10676279	E069	-2209
chr1	10723387	10724295	E069	44899
chr1	10725626	10725944	E069	47138
chr1	10725989	10726476	E069	47501
chr1	10639682	10639816	E070	-38672
chr1	10657285	10657517	E070	-20971
chr1	10657636	10657777	E070	-20711
chr1	10657802	10657902	E070	-20586
chr1	10658122	10658519	E070	-19969
chr1	10658521	10658674	E070	-19814
chr1	10658819	10658900	E070	-19588
chr1	10659286	10659975	E070	-18513
chr1	10675435	10675632	E070	-2856
chr1	10676080	10676130	E070	-2358
chr1	10676190	10676279	E070	-2209
chr1	10676383	10676433	E070	-2055
chr1	10683745	10683802	E070	5257
chr1	10692059	10692263	E070	13571
chr1	10692491	10692700	E070	14003
chr1	10692869	10693116	E070	14381
chr1	10694645	10695194	E070	16157
chr1	10695242	10696319	E070	16754
chr1	10699890	10700675	E070	21402
chr1	10700718	10700866	E070	22230
chr1	10700912	10701033	E070	22424
chr1	10701085	10701135	E070	22597
chr1	10701359	10701479	E070	22871
chr1	10708766	10708816	E070	30278
chr1	10711529	10711737	E070	33041
chr1	10711855	10712174	E070	33367
chr1	10723007	10723313	E070	44519
chr1	10723387	10724295	E070	44899
chr1	10724441	10724697	E070	45953
chr1	10658122	10658519	E071	-19969
chr1	10658521	10658674	E071	-19814
chr1	10674173	10674224	E071	-4264
chr1	10674618	10674691	E071	-3797
chr1	10675435	10675632	E071	-2856
chr1	10676080	10676130	E071	-2358
chr1	10676190	10676279	E071	-2209
chr1	10694645	10695194	E071	16157
chr1	10695242	10696319	E071	16754
chr1	10700718	10700866	E071	22230
chr1	10700912	10701033	E071	22424
chr1	10701085	10701135	E071	22597
chr1	10723007	10723313	E071	44519
chr1	10723387	10724295	E071	44899
chr1	10725626	10725944	E071	47138
chr1	10725989	10726476	E071	47501
chr1	10658122	10658519	E072	-19969
chr1	10674618	10674691	E072	-3797
chr1	10676080	10676130	E072	-2358
chr1	10676190	10676279	E072	-2209
chr1	10723007	10723313	E072	44519
chr1	10723387	10724295	E072	44899
chr1	10724441	10724697	E072	45953
chr1	10725626	10725944	E072	47138
chr1	10725989	10726476	E072	47501
chr1	10658122	10658519	E073	-19969
chr1	10694645	10695194	E073	16157
chr1	10723007	10723313	E073	44519
chr1	10723387	10724295	E073	44899
chr1	10658122	10658519	E074	-19969
chr1	10674618	10674691	E074	-3797
chr1	10723387	10724295	E074	44899
chr1	10725626	10725944	E074	47138
chr1	10725989	10726476	E074	47501
chr1	10726487	10726755	E074	47999
chr1	10672536	10673120	E081	-5368
chr1	10675435	10675632	E081	-2856
chr1	10676080	10676130	E081	-2358
chr1	10676190	10676279	E081	-2209
chr1	10676383	10676433	E081	-2055
chr1	10695242	10696319	E081	16754
chr1	10699890	10700675	E081	21402
chr1	10700718	10700866	E081	22230
chr1	10700912	10701033	E081	22424
chr1	10711529	10711737	E081	33041
chr1	10711855	10712174	E081	33367
chr1	10722583	10722820	E081	44095
chr1	10722892	10722989	E081	44404
chr1	10723007	10723313	E081	44519
chr1	10723387	10724295	E081	44899
chr1	10724441	10724697	E081	45953
chr1	10652230	10652294	E082	-26194
chr1	10675435	10675632	E082	-2856
chr1	10694645	10695194	E082	16157
chr1	10695242	10696319	E082	16754
chr1	10723387	10724295	E082	44899
chr1	10724441	10724697	E082	45953

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	20325
chr1	10698970	10699106	E070	20482
chr1	10699129	10699276	E070	20641
chr1	10698304	10698417	E082	19816
chr1	10698437	10698582	E082	19949
chr1	10698617	10698657	E082	20129
chr1	10698725	10698803	E082	20237
chr1	10698813	10698918	E082	20325
chr1	10698970	10699106	E082	20482
chr1	10699129	10699276	E082	20641