rs4329572

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

TOMM20 : Intron Variant
SNORA14B : 500B Downstream Variant
LOC105379283 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0276 (8267/29954,GnomAD)
C==0271 (7898/29116,TOPMED)
C==0339 (1697/5008,1000G)
C==0323 (1243/3854,ALSPAC)
C==0345 (1279/3708,TWINSUK)

Position: chr1:235127607 (GRCh38.p7) (1q42.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 71 Enhancers around

Promoter: 69 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.235127607C>A
GRCh37.p13 chr 1	NC_000001.10:g.235290922C>A

Gene: TOMM20, translocase of outer mitochondrial membrane 20(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TOMM20 transcript	NM_014765.2:c.	N/A	Intron Variant

Gene: SNORA14B, small nucleolar RNA, H/ACA box 14B(minus strand): 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SNORA14B transcript	NR_002956.1:n.	N/A	Downstream Transcript Variant

Gene: LOC105379283, uncharacterized LOC105379283(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105379283 transcript	XR_949295.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.127	A=0.873
1000Genomes	American	Sub	694	C=0.360	A=0.640
1000Genomes	East Asian	Sub	1008	C=0.633	A=0.367
1000Genomes	Europe	Sub	1006	C=0.329	A=0.671
1000Genomes	Global	Study-wide	5008	C=0.339	A=0.661
1000Genomes	South Asian	Sub	978	C=0.320	A=0.680
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.323	A=0.677
The Genome Aggregation Database	African	Sub	8714	C=0.146	A=0.854
The Genome Aggregation Database	American	Sub	832	C=0.370	A=0.630
The Genome Aggregation Database	East Asian	Sub	1618	C=0.624	A=0.376
The Genome Aggregation Database	Europe	Sub	18488	C=0.302	A=0.697
The Genome Aggregation Database	Global	Study-wide	29954	C=0.276	A=0.724
The Genome Aggregation Database	Other	Sub	302	C=0.290	A=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.271	A=0.728
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.345	A=0.655

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs4329572	0.0001	alcoholism (heaviness of drinking)	21529783

eQTL of rs4329572 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 rs4329572 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	235242210	235243684	E067	-47238
chr1	235246336	235247684	E067	-43238
chr1	235253609	235254440	E067	-36482
chr1	235254535	235254595	E067	-36327
chr1	235256311	235256406	E067	-34516
chr1	235286020	235286060	E067	-4862
chr1	235319971	235320377	E067	29049
chr1	235320454	235320609	E067	29532
chr1	235320772	235320828	E067	29850
chr1	235253609	235254440	E068	-36482
chr1	235254535	235254595	E068	-36327
chr1	235325457	235325545	E068	34535
chr1	235242210	235243684	E069	-47238
chr1	235246213	235246294	E069	-44628
chr1	235246336	235247684	E069	-43238
chr1	235253609	235254440	E069	-36482
chr1	235254535	235254595	E069	-36327
chr1	235256311	235256406	E069	-34516
chr1	235267265	235267347	E069	-23575
chr1	235268170	235268811	E069	-22111
chr1	235322897	235322951	E069	31975
chr1	235323184	235323228	E069	32262
chr1	235323294	235323338	E069	32372
chr1	235325457	235325545	E069	34535
chr1	235246336	235247684	E070	-43238
chr1	235268170	235268811	E070	-22111
chr1	235322601	235322657	E070	31679
chr1	235322897	235322951	E070	31975
chr1	235323184	235323228	E070	32262
chr1	235242210	235243684	E071	-47238
chr1	235246213	235246294	E071	-44628
chr1	235253609	235254440	E071	-36482
chr1	235254535	235254595	E071	-36327
chr1	235267265	235267347	E071	-23575
chr1	235286020	235286060	E071	-4862
chr1	235286497	235286552	E071	-4370
chr1	235286798	235286930	E071	-3992
chr1	235323184	235323228	E071	32262
chr1	235323294	235323338	E071	32372
chr1	235325457	235325545	E071	34535
chr1	235253609	235254440	E072	-36482
chr1	235254535	235254595	E072	-36327
chr1	235256311	235256406	E072	-34516
chr1	235323184	235323228	E072	32262
chr1	235323294	235323338	E072	32372
chr1	235325457	235325545	E072	34535
chr1	235242210	235243684	E073	-47238
chr1	235246336	235247684	E073	-43238
chr1	235253609	235254440	E073	-36482
chr1	235267265	235267347	E073	-23575
chr1	235242210	235243684	E074	-47238
chr1	235246336	235247684	E074	-43238
chr1	235253609	235254440	E074	-36482
chr1	235256311	235256406	E074	-34516
chr1	235285799	235285900	E074	-5022
chr1	235286020	235286060	E074	-4862
chr1	235325457	235325545	E074	34535
chr1	235242210	235243684	E081	-47238
chr1	235246336	235247684	E081	-43238
chr1	235253609	235254440	E081	-36482
chr1	235266414	235266698	E081	-24224
chr1	235267065	235267154	E081	-23768
chr1	235267265	235267347	E081	-23575
chr1	235322601	235322657	E081	31679
chr1	235322897	235322951	E081	31975
chr1	235323184	235323228	E081	32262
chr1	235323294	235323338	E081	32372
chr1	235325457	235325545	E081	34535
chr1	235242210	235243684	E082	-47238
chr1	235246336	235247684	E082	-43238
chr1	235253609	235254440	E082	-36482

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	235290575	235290723	E067	-199
chr1	235290778	235290898	E067	-24
chr1	235290915	235291041	E067	0
chr1	235291046	235291291	E067	124
chr1	235291322	235291413	E067	400
chr1	235291467	235292726	E067	545
chr1	235323841	235325247	E067	32919
chr1	235290575	235290723	E068	-199
chr1	235290778	235290898	E068	-24
chr1	235290915	235291041	E068	0
chr1	235291046	235291291	E068	124
chr1	235291322	235291413	E068	400
chr1	235291467	235292726	E068	545
chr1	235323841	235325247	E068	32919
chr1	235290575	235290723	E069	-199
chr1	235290778	235290898	E069	-24
chr1	235290915	235291041	E069	0
chr1	235291046	235291291	E069	124
chr1	235291322	235291413	E069	400
chr1	235291467	235292726	E069	545
chr1	235323841	235325247	E069	32919
chr1	235290575	235290723	E070	-199
chr1	235290778	235290898	E070	-24
chr1	235290915	235291041	E070	0
chr1	235291046	235291291	E070	124
chr1	235291322	235291413	E070	400
chr1	235291467	235292726	E070	545
chr1	235323841	235325247	E070	32919
chr1	235290575	235290723	E071	-199
chr1	235290778	235290898	E071	-24
chr1	235290915	235291041	E071	0
chr1	235291046	235291291	E071	124
chr1	235291322	235291413	E071	400
chr1	235291467	235292726	E071	545
chr1	235323841	235325247	E071	32919
chr1	235290575	235290723	E072	-199
chr1	235290778	235290898	E072	-24
chr1	235290915	235291041	E072	0
chr1	235291046	235291291	E072	124
chr1	235291322	235291413	E072	400
chr1	235291467	235292726	E072	545
chr1	235323841	235325247	E072	32919
chr1	235290575	235290723	E073	-199
chr1	235290778	235290898	E073	-24
chr1	235290915	235291041	E073	0
chr1	235291046	235291291	E073	124
chr1	235291322	235291413	E073	400
chr1	235291467	235292726	E073	545
chr1	235323841	235325247	E073	32919
chr1	235290778	235290898	E074	-24
chr1	235290915	235291041	E074	0
chr1	235291046	235291291	E074	124
chr1	235291322	235291413	E074	400
chr1	235291467	235292726	E074	545
chr1	235323841	235325247	E074	32919
chr1	235290575	235290723	E081	-199
chr1	235290778	235290898	E081	-24
chr1	235290915	235291041	E081	0
chr1	235291046	235291291	E081	124
chr1	235291322	235291413	E081	400
chr1	235291467	235292726	E081	545
chr1	235323841	235325247	E081	32919
chr1	235290575	235290723	E082	-199
chr1	235290778	235290898	E082	-24
chr1	235290915	235291041	E082	0
chr1	235291046	235291291	E082	124
chr1	235291322	235291413	E082	400
chr1	235291467	235292726	E082	545
chr1	235323841	235325247	E082	32919