rs11121599

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0333 (9977/29936,GnomAD)
A==0360 (10505/29118,TOPMED)
A==0401 (2006/5008,1000G)
A==0205 (791/3854,ALSPAC)
A==0213 (791/3708,TWINSUK)

Position: chr1:10606678 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 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.10606678A>G
GRCh37.p13 chr 1	NC_000001.10:g.10666735A>G
PEX14 RefSeqGene	NG_008340.1:g.136733A>G

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=0.635	G=0.365
1000Genomes	American	Sub	694	A=0.220	G=0.780
1000Genomes	East Asian	Sub	1008	A=0.412	G=0.588
1000Genomes	Europe	Sub	1006	A=0.217	G=0.783
1000Genomes	Global	Study-wide	5008	A=0.401	G=0.599
1000Genomes	South Asian	Sub	978	A=0.390	G=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.205	G=0.795
The Genome Aggregation Database	African	Sub	8698	A=0.549	G=0.451
The Genome Aggregation Database	American	Sub	836	A=0.190	G=0.810
The Genome Aggregation Database	East Asian	Sub	1620	A=0.423	G=0.577
The Genome Aggregation Database	Europe	Sub	18480	A=0.231	G=0.768
The Genome Aggregation Database	Global	Study-wide	29936	A=0.333	G=0.666
The Genome Aggregation Database	Other	Sub	302	A=0.250	G=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.360	G=0.639
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.213	G=0.787

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
rs11121599	3.08E-06	alcohol dependence (age at onset)	24962325

eQTL of rs11121599 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 rs11121599 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	7883
chr1	10676080	10676130	E067	9345
chr1	10676190	10676279	E067	9455
chr1	10619744	10619845	E068	-46890
chr1	10658122	10658519	E068	-8216
chr1	10674618	10674691	E068	7883
chr1	10674618	10674691	E069	7883
chr1	10676080	10676130	E069	9345
chr1	10676190	10676279	E069	9455
chr1	10639682	10639816	E070	-26919
chr1	10657285	10657517	E070	-9218
chr1	10657636	10657777	E070	-8958
chr1	10657802	10657902	E070	-8833
chr1	10658122	10658519	E070	-8216
chr1	10658521	10658674	E070	-8061
chr1	10658819	10658900	E070	-7835
chr1	10659286	10659975	E070	-6760
chr1	10675435	10675632	E070	8700
chr1	10676080	10676130	E070	9345
chr1	10676190	10676279	E070	9455
chr1	10676383	10676433	E070	9648
chr1	10683745	10683802	E070	17010
chr1	10692059	10692263	E070	25324
chr1	10692491	10692700	E070	25756
chr1	10692869	10693116	E070	26134
chr1	10694645	10695194	E070	27910
chr1	10695242	10696319	E070	28507
chr1	10699890	10700675	E070	33155
chr1	10700718	10700866	E070	33983
chr1	10700912	10701033	E070	34177
chr1	10701085	10701135	E070	34350
chr1	10701359	10701479	E070	34624
chr1	10708766	10708816	E070	42031
chr1	10711529	10711737	E070	44794
chr1	10711855	10712174	E070	45120
chr1	10619540	10619590	E071	-47145
chr1	10619744	10619845	E071	-46890
chr1	10658122	10658519	E071	-8216
chr1	10658521	10658674	E071	-8061
chr1	10674173	10674224	E071	7438
chr1	10674618	10674691	E071	7883
chr1	10675435	10675632	E071	8700
chr1	10676080	10676130	E071	9345
chr1	10676190	10676279	E071	9455
chr1	10694645	10695194	E071	27910
chr1	10695242	10696319	E071	28507
chr1	10700718	10700866	E071	33983
chr1	10700912	10701033	E071	34177
chr1	10701085	10701135	E071	34350
chr1	10619540	10619590	E072	-47145
chr1	10619744	10619845	E072	-46890
chr1	10658122	10658519	E072	-8216
chr1	10674618	10674691	E072	7883
chr1	10676080	10676130	E072	9345
chr1	10676190	10676279	E072	9455
chr1	10658122	10658519	E073	-8216
chr1	10694645	10695194	E073	27910
chr1	10619744	10619845	E074	-46890
chr1	10658122	10658519	E074	-8216
chr1	10674618	10674691	E074	7883
chr1	10672536	10673120	E081	5801
chr1	10675435	10675632	E081	8700
chr1	10676080	10676130	E081	9345
chr1	10676190	10676279	E081	9455
chr1	10676383	10676433	E081	9648
chr1	10695242	10696319	E081	28507
chr1	10699890	10700675	E081	33155
chr1	10700718	10700866	E081	33983
chr1	10700912	10701033	E081	34177
chr1	10711529	10711737	E081	44794
chr1	10711855	10712174	E081	45120
chr1	10652230	10652294	E082	-14441
chr1	10675435	10675632	E082	8700
chr1	10694645	10695194	E082	27910
chr1	10695242	10696319	E082	28507

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	32078
chr1	10698970	10699106	E070	32235
chr1	10699129	10699276	E070	32394
chr1	10698304	10698417	E082	31569
chr1	10698437	10698582	E082	31702
chr1	10698617	10698657	E082	31882
chr1	10698725	10698803	E082	31990
chr1	10698813	10698918	E082	32078
chr1	10698970	10699106	E082	32235
chr1	10699129	10699276	E082	32394