rs284303

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PEX14 : 500B Downstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0212 (6346/29934,GnomAD)
T=0235 (6865/29118,TOPMED)
T=0209 (1047/5008,1000G)
T=0118 (455/3854,ALSPAC)
T=0128 (473/3708,TWINSUK)

Position: chr1:10630826 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 125 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.10630826C>T
GRCh37.p13 chr 1	NC_000001.10:g.10690883C>T
PEX14 RefSeqGene	NG_008340.1:g.160881C>T

Gene: PEX14, peroxisomal biogenesis factor 14(plus strand): 500B Downstream Variant

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.583	T=0.417
1000Genomes	American	Sub	694	C=0.860	T=0.140
1000Genomes	East Asian	Sub	1008	C=0.943	T=0.057
1000Genomes	Europe	Sub	1006	C=0.847	T=0.153
1000Genomes	Global	Study-wide	5008	C=0.791	T=0.209
1000Genomes	South Asian	Sub	978	C=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.882	T=0.118
The Genome Aggregation Database	African	Sub	8714	C=0.643	T=0.357
The Genome Aggregation Database	American	Sub	836	C=0.870	T=0.130
The Genome Aggregation Database	East Asian	Sub	1622	C=0.908	T=0.092
The Genome Aggregation Database	Europe	Sub	18460	C=0.841	T=0.158
The Genome Aggregation Database	Global	Study-wide	29934	C=0.788	T=0.212
The Genome Aggregation Database	Other	Sub	302	C=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.764	T=0.235
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.872	T=0.128

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
rs284303	9.06E-07	alcohol dependence (age at onset)	24962325

eQTL of rs284303 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 rs284303 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	-16192
chr1	10676080	10676130	E067	-14753
chr1	10676190	10676279	E067	-14604
chr1	10723387	10724295	E067	32504
chr1	10725989	10726476	E067	35106
chr1	10658122	10658519	E068	-32364
chr1	10674618	10674691	E068	-16192
chr1	10723387	10724295	E068	32504
chr1	10674618	10674691	E069	-16192
chr1	10676080	10676130	E069	-14753
chr1	10676190	10676279	E069	-14604
chr1	10723387	10724295	E069	32504
chr1	10725626	10725944	E069	34743
chr1	10725989	10726476	E069	35106
chr1	10657285	10657517	E070	-33366
chr1	10657636	10657777	E070	-33106
chr1	10657802	10657902	E070	-32981
chr1	10658122	10658519	E070	-32364
chr1	10658521	10658674	E070	-32209
chr1	10658819	10658900	E070	-31983
chr1	10659286	10659975	E070	-30908
chr1	10675435	10675632	E070	-15251
chr1	10676080	10676130	E070	-14753
chr1	10676190	10676279	E070	-14604
chr1	10676383	10676433	E070	-14450
chr1	10683745	10683802	E070	-7081
chr1	10692059	10692263	E070	1176
chr1	10692491	10692700	E070	1608
chr1	10692869	10693116	E070	1986
chr1	10694645	10695194	E070	3762
chr1	10695242	10696319	E070	4359
chr1	10699890	10700675	E070	9007
chr1	10700718	10700866	E070	9835
chr1	10700912	10701033	E070	10029
chr1	10701085	10701135	E070	10202
chr1	10701359	10701479	E070	10476
chr1	10708766	10708816	E070	17883
chr1	10711529	10711737	E070	20646
chr1	10711855	10712174	E070	20972
chr1	10723007	10723313	E070	32124
chr1	10723387	10724295	E070	32504
chr1	10724441	10724697	E070	33558
chr1	10730791	10730871	E070	39908
chr1	10731201	10731514	E070	40318
chr1	10731564	10731686	E070	40681
chr1	10731720	10732119	E070	40837
chr1	10733491	10733680	E070	42608
chr1	10734074	10734134	E070	43191
chr1	10734771	10734824	E070	43888
chr1	10735138	10735403	E070	44255
chr1	10735523	10735640	E070	44640
chr1	10737231	10738061	E070	46348
chr1	10738134	10738259	E070	47251
chr1	10738329	10738466	E070	47446
chr1	10738761	10738860	E070	47878
chr1	10738967	10740291	E070	48084
chr1	10658122	10658519	E071	-32364
chr1	10658521	10658674	E071	-32209
chr1	10674173	10674224	E071	-16659
chr1	10674618	10674691	E071	-16192
chr1	10675435	10675632	E071	-15251
chr1	10676080	10676130	E071	-14753
chr1	10676190	10676279	E071	-14604
chr1	10694645	10695194	E071	3762
chr1	10695242	10696319	E071	4359
chr1	10700718	10700866	E071	9835
chr1	10700912	10701033	E071	10029
chr1	10701085	10701135	E071	10202
chr1	10723007	10723313	E071	32124
chr1	10723387	10724295	E071	32504
chr1	10725626	10725944	E071	34743
chr1	10725989	10726476	E071	35106
chr1	10658122	10658519	E072	-32364
chr1	10674618	10674691	E072	-16192
chr1	10676080	10676130	E072	-14753
chr1	10676190	10676279	E072	-14604
chr1	10723007	10723313	E072	32124
chr1	10723387	10724295	E072	32504
chr1	10724441	10724697	E072	33558
chr1	10725626	10725944	E072	34743
chr1	10725989	10726476	E072	35106
chr1	10658122	10658519	E073	-32364
chr1	10694645	10695194	E073	3762
chr1	10723007	10723313	E073	32124
chr1	10723387	10724295	E073	32504
chr1	10658122	10658519	E074	-32364
chr1	10674618	10674691	E074	-16192
chr1	10723387	10724295	E074	32504
chr1	10725626	10725944	E074	34743
chr1	10725989	10726476	E074	35106
chr1	10726487	10726755	E074	35604
chr1	10672536	10673120	E081	-17763
chr1	10675435	10675632	E081	-15251
chr1	10676080	10676130	E081	-14753
chr1	10676190	10676279	E081	-14604
chr1	10676383	10676433	E081	-14450
chr1	10695242	10696319	E081	4359
chr1	10699890	10700675	E081	9007
chr1	10700718	10700866	E081	9835
chr1	10700912	10701033	E081	10029
chr1	10711529	10711737	E081	20646
chr1	10711855	10712174	E081	20972
chr1	10722583	10722820	E081	31700
chr1	10722892	10722989	E081	32009
chr1	10723007	10723313	E081	32124
chr1	10723387	10724295	E081	32504
chr1	10724441	10724697	E081	33558
chr1	10731201	10731514	E081	40318
chr1	10731564	10731686	E081	40681
chr1	10731720	10732119	E081	40837
chr1	10733491	10733680	E081	42608
chr1	10737231	10738061	E081	46348
chr1	10738134	10738259	E081	47251
chr1	10738329	10738466	E081	47446
chr1	10738761	10738860	E081	47878
chr1	10738967	10740291	E081	48084
chr1	10652230	10652294	E082	-38589
chr1	10675435	10675632	E082	-15251
chr1	10694645	10695194	E082	3762
chr1	10695242	10696319	E082	4359
chr1	10723387	10724295	E082	32504
chr1	10724441	10724697	E082	33558
chr1	10738134	10738259	E082	47251
chr1	10738329	10738466	E082	47446
chr1	10738761	10738860	E082	47878

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	7930
chr1	10698970	10699106	E070	8087
chr1	10699129	10699276	E070	8246
chr1	10698304	10698417	E082	7421
chr1	10698437	10698582	E082	7554
chr1	10698617	10698657	E082	7734
chr1	10698725	10698803	E082	7842
chr1	10698813	10698918	E082	7930
chr1	10698970	10699106	E082	8087
chr1	10699129	10699276	E082	8246