rs185864

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

PEX14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0199 (5967/29952,GnomAD)
C=0216 (6298/29118,TOPMED)
C=0197 (985/5008,1000G)
C=0119 (458/3854,ALSPAC)
C=0128 (475/3708,TWINSUK)

Position: chr1:10627669 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 113 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.10627669G>C
GRCh37.p13 chr 1	NC_000001.10:g.10687726G>C
PEX14 RefSeqGene	NG_008340.1:g.157724G>C

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=0.629	C=0.371
1000Genomes	American	Sub	694	G=0.860	C=0.140
1000Genomes	East Asian	Sub	1008	G=0.942	C=0.058
1000Genomes	Europe	Sub	1006	G=0.848	C=0.152
1000Genomes	Global	Study-wide	5008	G=0.803	C=0.197
1000Genomes	South Asian	Sub	978	G=0.810	C=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.881	C=0.119
The Genome Aggregation Database	African	Sub	8718	G=0.688	C=0.312
The Genome Aggregation Database	American	Sub	836	G=0.880	C=0.120
The Genome Aggregation Database	East Asian	Sub	1620	G=0.907	C=0.093
The Genome Aggregation Database	Europe	Sub	18476	G=0.841	C=0.159
The Genome Aggregation Database	Global	Study-wide	29952	G=0.800	C=0.199
The Genome Aggregation Database	Other	Sub	302	G=0.810	C=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.783	C=0.216
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.872	C=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
rs185864	9.06E-07	alcohol dependence (age at onset)	24962325

eQTL of rs185864 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 rs185864 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	-13035
chr1	10676080	10676130	E067	-11596
chr1	10676190	10676279	E067	-11447
chr1	10723387	10724295	E067	35661
chr1	10725989	10726476	E067	38263
chr1	10658122	10658519	E068	-29207
chr1	10674618	10674691	E068	-13035
chr1	10723387	10724295	E068	35661
chr1	10674618	10674691	E069	-13035
chr1	10676080	10676130	E069	-11596
chr1	10676190	10676279	E069	-11447
chr1	10723387	10724295	E069	35661
chr1	10725626	10725944	E069	37900
chr1	10725989	10726476	E069	38263
chr1	10639682	10639816	E070	-47910
chr1	10657285	10657517	E070	-30209
chr1	10657636	10657777	E070	-29949
chr1	10657802	10657902	E070	-29824
chr1	10658122	10658519	E070	-29207
chr1	10658521	10658674	E070	-29052
chr1	10658819	10658900	E070	-28826
chr1	10659286	10659975	E070	-27751
chr1	10675435	10675632	E070	-12094
chr1	10676080	10676130	E070	-11596
chr1	10676190	10676279	E070	-11447
chr1	10676383	10676433	E070	-11293
chr1	10683745	10683802	E070	-3924
chr1	10692059	10692263	E070	4333
chr1	10692491	10692700	E070	4765
chr1	10692869	10693116	E070	5143
chr1	10694645	10695194	E070	6919
chr1	10695242	10696319	E070	7516
chr1	10699890	10700675	E070	12164
chr1	10700718	10700866	E070	12992
chr1	10700912	10701033	E070	13186
chr1	10701085	10701135	E070	13359
chr1	10701359	10701479	E070	13633
chr1	10708766	10708816	E070	21040
chr1	10711529	10711737	E070	23803
chr1	10711855	10712174	E070	24129
chr1	10723007	10723313	E070	35281
chr1	10723387	10724295	E070	35661
chr1	10724441	10724697	E070	36715
chr1	10730791	10730871	E070	43065
chr1	10731201	10731514	E070	43475
chr1	10731564	10731686	E070	43838
chr1	10731720	10732119	E070	43994
chr1	10733491	10733680	E070	45765
chr1	10734074	10734134	E070	46348
chr1	10734771	10734824	E070	47045
chr1	10735138	10735403	E070	47412
chr1	10735523	10735640	E070	47797
chr1	10658122	10658519	E071	-29207
chr1	10658521	10658674	E071	-29052
chr1	10674173	10674224	E071	-13502
chr1	10674618	10674691	E071	-13035
chr1	10675435	10675632	E071	-12094
chr1	10676080	10676130	E071	-11596
chr1	10676190	10676279	E071	-11447
chr1	10694645	10695194	E071	6919
chr1	10695242	10696319	E071	7516
chr1	10700718	10700866	E071	12992
chr1	10700912	10701033	E071	13186
chr1	10701085	10701135	E071	13359
chr1	10723007	10723313	E071	35281
chr1	10723387	10724295	E071	35661
chr1	10725626	10725944	E071	37900
chr1	10725989	10726476	E071	38263
chr1	10658122	10658519	E072	-29207
chr1	10674618	10674691	E072	-13035
chr1	10676080	10676130	E072	-11596
chr1	10676190	10676279	E072	-11447
chr1	10723007	10723313	E072	35281
chr1	10723387	10724295	E072	35661
chr1	10724441	10724697	E072	36715
chr1	10725626	10725944	E072	37900
chr1	10725989	10726476	E072	38263
chr1	10658122	10658519	E073	-29207
chr1	10694645	10695194	E073	6919
chr1	10723007	10723313	E073	35281
chr1	10723387	10724295	E073	35661
chr1	10658122	10658519	E074	-29207
chr1	10674618	10674691	E074	-13035
chr1	10723387	10724295	E074	35661
chr1	10725626	10725944	E074	37900
chr1	10725989	10726476	E074	38263
chr1	10726487	10726755	E074	38761
chr1	10672536	10673120	E081	-14606
chr1	10675435	10675632	E081	-12094
chr1	10676080	10676130	E081	-11596
chr1	10676190	10676279	E081	-11447
chr1	10676383	10676433	E081	-11293
chr1	10695242	10696319	E081	7516
chr1	10699890	10700675	E081	12164
chr1	10700718	10700866	E081	12992
chr1	10700912	10701033	E081	13186
chr1	10711529	10711737	E081	23803
chr1	10711855	10712174	E081	24129
chr1	10722583	10722820	E081	34857
chr1	10722892	10722989	E081	35166
chr1	10723007	10723313	E081	35281
chr1	10723387	10724295	E081	35661
chr1	10724441	10724697	E081	36715
chr1	10731201	10731514	E081	43475
chr1	10731564	10731686	E081	43838
chr1	10731720	10732119	E081	43994
chr1	10733491	10733680	E081	45765
chr1	10652230	10652294	E082	-35432
chr1	10675435	10675632	E082	-12094
chr1	10694645	10695194	E082	6919
chr1	10695242	10696319	E082	7516
chr1	10723387	10724295	E082	35661
chr1	10724441	10724697	E082	36715

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10698813	10698918	E070	11087
chr1	10698970	10699106	E070	11244
chr1	10699129	10699276	E070	11403
chr1	10698304	10698417	E082	10578
chr1	10698437	10698582	E082	10711
chr1	10698617	10698657	E082	10891
chr1	10698725	10698803	E082	10999
chr1	10698813	10698918	E082	11087
chr1	10698970	10699106	E082	11244
chr1	10699129	10699276	E082	11403