rs190775

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0199 (5972/29940,GnomAD)
T=0218 (6348/29118,TOPMED)
T=0198 (990/5008,1000G)
T=0119 (457/3854,ALSPAC)
T=0128 (476/3708,TWINSUK)

Position: chr1:10623626 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 109 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.10623626G>T
GRCh37.p13 chr 1	NC_000001.10:g.10683683G>T
PEX14 RefSeqGene	NG_008340.1:g.153681G>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	G=0.625	T=0.375
1000Genomes	American	Sub	694	G=0.860	T=0.140
1000Genomes	East Asian	Sub	1008	G=0.942	T=0.058
1000Genomes	Europe	Sub	1006	G=0.848	T=0.152
1000Genomes	Global	Study-wide	5008	G=0.802	T=0.198
1000Genomes	South Asian	Sub	978	G=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.881	T=0.119
The Genome Aggregation Database	African	Sub	8704	G=0.685	T=0.315
The Genome Aggregation Database	American	Sub	838	G=0.870	T=0.130
The Genome Aggregation Database	East Asian	Sub	1622	G=0.907	T=0.093
The Genome Aggregation Database	Europe	Sub	18474	G=0.841	T=0.158
The Genome Aggregation Database	Global	Study-wide	29940	G=0.800	T=0.199
The Genome Aggregation Database	Other	Sub	302	G=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.782	T=0.218
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=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
rs190775	2.39E-06	alcohol dependence (age at onset)	24962325

eQTL of rs190775 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 rs190775 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	-8992
chr1	10676080	10676130	E067	-7553
chr1	10676190	10676279	E067	-7404
chr1	10723387	10724295	E067	39704
chr1	10725989	10726476	E067	42306
chr1	10658122	10658519	E068	-25164
chr1	10674618	10674691	E068	-8992
chr1	10723387	10724295	E068	39704
chr1	10674618	10674691	E069	-8992
chr1	10676080	10676130	E069	-7553
chr1	10676190	10676279	E069	-7404
chr1	10723387	10724295	E069	39704
chr1	10725626	10725944	E069	41943
chr1	10725989	10726476	E069	42306
chr1	10639682	10639816	E070	-43867
chr1	10657285	10657517	E070	-26166
chr1	10657636	10657777	E070	-25906
chr1	10657802	10657902	E070	-25781
chr1	10658122	10658519	E070	-25164
chr1	10658521	10658674	E070	-25009
chr1	10658819	10658900	E070	-24783
chr1	10659286	10659975	E070	-23708
chr1	10675435	10675632	E070	-8051
chr1	10676080	10676130	E070	-7553
chr1	10676190	10676279	E070	-7404
chr1	10676383	10676433	E070	-7250
chr1	10683745	10683802	E070	62
chr1	10692059	10692263	E070	8376
chr1	10692491	10692700	E070	8808
chr1	10692869	10693116	E070	9186
chr1	10694645	10695194	E070	10962
chr1	10695242	10696319	E070	11559
chr1	10699890	10700675	E070	16207
chr1	10700718	10700866	E070	17035
chr1	10700912	10701033	E070	17229
chr1	10701085	10701135	E070	17402
chr1	10701359	10701479	E070	17676
chr1	10708766	10708816	E070	25083
chr1	10711529	10711737	E070	27846
chr1	10711855	10712174	E070	28172
chr1	10723007	10723313	E070	39324
chr1	10723387	10724295	E070	39704
chr1	10724441	10724697	E070	40758
chr1	10730791	10730871	E070	47108
chr1	10731201	10731514	E070	47518
chr1	10731564	10731686	E070	47881
chr1	10731720	10732119	E070	48037
chr1	10733491	10733680	E070	49808
chr1	10658122	10658519	E071	-25164
chr1	10658521	10658674	E071	-25009
chr1	10674173	10674224	E071	-9459
chr1	10674618	10674691	E071	-8992
chr1	10675435	10675632	E071	-8051
chr1	10676080	10676130	E071	-7553
chr1	10676190	10676279	E071	-7404
chr1	10694645	10695194	E071	10962
chr1	10695242	10696319	E071	11559
chr1	10700718	10700866	E071	17035
chr1	10700912	10701033	E071	17229
chr1	10701085	10701135	E071	17402
chr1	10723007	10723313	E071	39324
chr1	10723387	10724295	E071	39704
chr1	10725626	10725944	E071	41943
chr1	10725989	10726476	E071	42306
chr1	10658122	10658519	E072	-25164
chr1	10674618	10674691	E072	-8992
chr1	10676080	10676130	E072	-7553
chr1	10676190	10676279	E072	-7404
chr1	10723007	10723313	E072	39324
chr1	10723387	10724295	E072	39704
chr1	10724441	10724697	E072	40758
chr1	10725626	10725944	E072	41943
chr1	10725989	10726476	E072	42306
chr1	10658122	10658519	E073	-25164
chr1	10694645	10695194	E073	10962
chr1	10723007	10723313	E073	39324
chr1	10723387	10724295	E073	39704
chr1	10658122	10658519	E074	-25164
chr1	10674618	10674691	E074	-8992
chr1	10723387	10724295	E074	39704
chr1	10725626	10725944	E074	41943
chr1	10725989	10726476	E074	42306
chr1	10726487	10726755	E074	42804
chr1	10672536	10673120	E081	-10563
chr1	10675435	10675632	E081	-8051
chr1	10676080	10676130	E081	-7553
chr1	10676190	10676279	E081	-7404
chr1	10676383	10676433	E081	-7250
chr1	10695242	10696319	E081	11559
chr1	10699890	10700675	E081	16207
chr1	10700718	10700866	E081	17035
chr1	10700912	10701033	E081	17229
chr1	10711529	10711737	E081	27846
chr1	10711855	10712174	E081	28172
chr1	10722583	10722820	E081	38900
chr1	10722892	10722989	E081	39209
chr1	10723007	10723313	E081	39324
chr1	10723387	10724295	E081	39704
chr1	10724441	10724697	E081	40758
chr1	10731201	10731514	E081	47518
chr1	10731564	10731686	E081	47881
chr1	10731720	10732119	E081	48037
chr1	10733491	10733680	E081	49808
chr1	10652230	10652294	E082	-31389
chr1	10675435	10675632	E082	-8051
chr1	10694645	10695194	E082	10962
chr1	10695242	10696319	E082	11559
chr1	10723387	10724295	E082	39704
chr1	10724441	10724697	E082	40758

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	15130
chr1	10698970	10699106	E070	15287
chr1	10699129	10699276	E070	15446
chr1	10698304	10698417	E082	14621
chr1	10698437	10698582	E082	14754
chr1	10698617	10698657	E082	14934
chr1	10698725	10698803	E082	15042
chr1	10698813	10698918	E082	15130
chr1	10698970	10699106	E082	15287
chr1	10699129	10699276	E082	15446