rs3790630

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0342 (10257/29922,GnomAD)
C==0371 (10811/29118,TOPMED)
C==0407 (2040/5008,1000G)
C==0210 (811/3854,ALSPAC)
C==0221 (819/3708,TWINSUK)

Position: chr1:10613037 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 71 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.10613037C>T
GRCh37.p13 chr 1	NC_000001.10:g.10673094C>T
PEX14 RefSeqGene	NG_008340.1:g.143092C>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	C=0.641	T=0.359
1000Genomes	American	Sub	694	C=0.220	T=0.780
1000Genomes	East Asian	Sub	1008	C=0.428	T=0.572
1000Genomes	Europe	Sub	1006	C=0.223	T=0.777
1000Genomes	Global	Study-wide	5008	C=0.407	T=0.593
1000Genomes	South Asian	Sub	978	C=0.390	T=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.210	T=0.790
The Genome Aggregation Database	African	Sub	8700	C=0.562	T=0.438
The Genome Aggregation Database	American	Sub	836	C=0.190	T=0.810
The Genome Aggregation Database	East Asian	Sub	1616	C=0.431	T=0.569
The Genome Aggregation Database	Europe	Sub	18468	C=0.240	T=0.759
The Genome Aggregation Database	Global	Study-wide	29922	C=0.342	T=0.657
The Genome Aggregation Database	Other	Sub	302	C=0.250	T=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.371	T=0.628
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.221	T=0.779

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
rs3790630	6.83E-06	alcohol dependence (age at onset)	24962325

eQTL of rs3790630 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 rs3790630 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	1524
chr1	10676080	10676130	E067	2986
chr1	10676190	10676279	E067	3096
chr1	10658122	10658519	E068	-14575
chr1	10674618	10674691	E068	1524
chr1	10674618	10674691	E069	1524
chr1	10676080	10676130	E069	2986
chr1	10676190	10676279	E069	3096
chr1	10639682	10639816	E070	-33278
chr1	10657285	10657517	E070	-15577
chr1	10657636	10657777	E070	-15317
chr1	10657802	10657902	E070	-15192
chr1	10658122	10658519	E070	-14575
chr1	10658521	10658674	E070	-14420
chr1	10658819	10658900	E070	-14194
chr1	10659286	10659975	E070	-13119
chr1	10675435	10675632	E070	2341
chr1	10676080	10676130	E070	2986
chr1	10676190	10676279	E070	3096
chr1	10676383	10676433	E070	3289
chr1	10683745	10683802	E070	10651
chr1	10692059	10692263	E070	18965
chr1	10692491	10692700	E070	19397
chr1	10692869	10693116	E070	19775
chr1	10694645	10695194	E070	21551
chr1	10695242	10696319	E070	22148
chr1	10699890	10700675	E070	26796
chr1	10700718	10700866	E070	27624
chr1	10700912	10701033	E070	27818
chr1	10701085	10701135	E070	27991
chr1	10701359	10701479	E070	28265
chr1	10708766	10708816	E070	35672
chr1	10711529	10711737	E070	38435
chr1	10711855	10712174	E070	38761
chr1	10658122	10658519	E071	-14575
chr1	10658521	10658674	E071	-14420
chr1	10674173	10674224	E071	1079
chr1	10674618	10674691	E071	1524
chr1	10675435	10675632	E071	2341
chr1	10676080	10676130	E071	2986
chr1	10676190	10676279	E071	3096
chr1	10694645	10695194	E071	21551
chr1	10695242	10696319	E071	22148
chr1	10700718	10700866	E071	27624
chr1	10700912	10701033	E071	27818
chr1	10701085	10701135	E071	27991
chr1	10658122	10658519	E072	-14575
chr1	10674618	10674691	E072	1524
chr1	10676080	10676130	E072	2986
chr1	10676190	10676279	E072	3096
chr1	10658122	10658519	E073	-14575
chr1	10694645	10695194	E073	21551
chr1	10658122	10658519	E074	-14575
chr1	10674618	10674691	E074	1524
chr1	10672536	10673120	E081	0
chr1	10675435	10675632	E081	2341
chr1	10676080	10676130	E081	2986
chr1	10676190	10676279	E081	3096
chr1	10676383	10676433	E081	3289
chr1	10695242	10696319	E081	22148
chr1	10699890	10700675	E081	26796
chr1	10700718	10700866	E081	27624
chr1	10700912	10701033	E081	27818
chr1	10711529	10711737	E081	38435
chr1	10711855	10712174	E081	38761
chr1	10722583	10722820	E081	49489
chr1	10722892	10722989	E081	49798
chr1	10652230	10652294	E082	-20800
chr1	10675435	10675632	E082	2341
chr1	10694645	10695194	E082	21551
chr1	10695242	10696319	E082	22148

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	25719
chr1	10698970	10699106	E070	25876
chr1	10699129	10699276	E070	26035
chr1	10698304	10698417	E082	25210
chr1	10698437	10698582	E082	25343
chr1	10698617	10698657	E082	25523
chr1	10698725	10698803	E082	25631
chr1	10698813	10698918	E082	25719
chr1	10698970	10699106	E082	25876
chr1	10699129	10699276	E082	26035