rs154148

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC105371084 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0465 (13942/29932,GnomAD)
C=0482 (14037/29118,TOPMED)
T==0459 (2301/5008,1000G)
C=0347 (1337/3854,ALSPAC)
C=0346 (1284/3708,TWINSUK)

Position: chr16:11862621 (GRCh38.p7) (16p13.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 98 Enhancers around

Promoter: 40 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 16	NC_000016.10:g.11862621T>C
GRCh37.p13 chr 16	NC_000016.9:g.11956478T>C

Gene: LOC105371084, uncharacterized LOC105371084(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371084 transcript variant X2	XR_001752085.1:n.	N/A	Intron Variant
LOC105371084 transcript variant X1	XR_933077.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.343	C=0.657
1000Genomes	American	Sub	694	T=0.570	C=0.430
1000Genomes	East Asian	Sub	1008	T=0.257	C=0.743
1000Genomes	Europe	Sub	1006	T=0.621	C=0.379
1000Genomes	Global	Study-wide	5008	T=0.459	C=0.541
1000Genomes	South Asian	Sub	978	T=0.580	C=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.653	C=0.347
The Genome Aggregation Database	African	Sub	8706	T=0.390	C=0.610
The Genome Aggregation Database	American	Sub	838	T=0.500	C=0.500
The Genome Aggregation Database	East Asian	Sub	1610	T=0.232	C=0.768
The Genome Aggregation Database	Europe	Sub	18478	T=0.627	C=0.372
The Genome Aggregation Database	Global	Study-wide	29932	T=0.534	C=0.465
The Genome Aggregation Database	Other	Sub	300	T=0.650	C=0.350
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.517	C=0.482
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.654	C=0.346

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

SNP ID	p-value	Traits	Study
rs154148	0.000797	alcohol consumption (maxi-drinks)	24277619

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr16:11956478	RP11-166B2.1	ENSG00000234719.4	T>C	0.0000e+0	-114022	Cerebellum
Chr16:11956478	RP11-166B2.1	ENSG00000234719.4	T>C	0.0000e+0	-114022	Cortex
Chr16:11956478	RP11-166B2.1	ENSG00000234719.4	T>C	0.0000e+0	-114022	Caudate_basal_ganglia

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 )
chr16	11948155	11948195	E067	-8283
chr16	11948383	11948423	E067	-8055
chr16	11948532	11948645	E067	-7833
chr16	12004064	12004412	E067	47586
chr16	12004528	12004642	E067	48050
chr16	12004736	12004822	E067	48258
chr16	12004836	12004880	E067	48358
chr16	12005102	12005191	E067	48624
chr16	11907653	11907848	E068	-48630
chr16	11918210	11918829	E068	-37649
chr16	11947773	11947879	E068	-8599
chr16	11948155	11948195	E068	-8283
chr16	11948383	11948423	E068	-8055
chr16	11948532	11948645	E068	-7833
chr16	11990563	11990629	E068	34085
chr16	11990695	11991122	E068	34217
chr16	12004064	12004412	E068	47586
chr16	12004528	12004642	E068	48050
chr16	12004736	12004822	E068	48258
chr16	12004836	12004880	E068	48358
chr16	12005102	12005191	E068	48624
chr16	12006332	12006427	E068	49854
chr16	11948383	11948423	E069	-8055
chr16	11948532	11948645	E069	-7833
chr16	11949402	11949536	E069	-6942
chr16	11949598	11949658	E069	-6820
chr16	11959080	11959141	E069	2602
chr16	12004064	12004412	E069	47586
chr16	12004528	12004642	E069	48050
chr16	12004736	12004822	E069	48258
chr16	12004836	12004880	E069	48358
chr16	11946926	11947000	E070	-9478
chr16	11947166	11947244	E070	-9234
chr16	11947773	11947879	E070	-8599
chr16	11948155	11948195	E070	-8283
chr16	11948383	11948423	E070	-8055
chr16	11948532	11948645	E070	-7833
chr16	11990563	11990629	E070	34085
chr16	11918210	11918829	E071	-37649
chr16	11947773	11947879	E071	-8599
chr16	11948155	11948195	E071	-8283
chr16	11948383	11948423	E071	-8055
chr16	11948532	11948645	E071	-7833
chr16	11958897	11958947	E071	2419
chr16	11959080	11959141	E071	2602
chr16	11959213	11959360	E071	2735
chr16	11990563	11990629	E071	34085
chr16	11990695	11991122	E071	34217
chr16	12004064	12004412	E071	47586
chr16	12004528	12004642	E071	48050
chr16	12004736	12004822	E071	48258
chr16	12004836	12004880	E071	48358
chr16	12006332	12006427	E071	49854
chr16	11966931	11966985	E072	10453
chr16	12002947	12003216	E072	46469
chr16	12003228	12003285	E072	46750
chr16	12003389	12003447	E072	46911
chr16	12003666	12003753	E072	47188
chr16	12004064	12004412	E072	47586
chr16	12004528	12004642	E072	48050
chr16	12004736	12004822	E072	48258
chr16	12004836	12004880	E072	48358
chr16	11918210	11918829	E073	-37649
chr16	11942755	11943086	E073	-13392
chr16	11943155	11943241	E073	-13237
chr16	12001042	12001092	E073	44564
chr16	12001096	12001161	E073	44618
chr16	12001417	12001606	E073	44939
chr16	12001635	12001757	E073	45157
chr16	12004064	12004412	E073	47586
chr16	12004528	12004642	E073	48050
chr16	12004736	12004822	E073	48258
chr16	12004836	12004880	E073	48358
chr16	12005102	12005191	E073	48624
chr16	12005224	12005321	E073	48746
chr16	11947773	11947879	E074	-8599
chr16	11948155	11948195	E074	-8283
chr16	11948383	11948423	E074	-8055
chr16	11948532	11948645	E074	-7833
chr16	11965120	11965373	E074	8642
chr16	11965488	11965592	E074	9010
chr16	12004528	12004642	E074	48050
chr16	12004736	12004822	E074	48258
chr16	12004836	12004880	E074	48358
chr16	11946926	11947000	E081	-9478
chr16	11947166	11947244	E081	-9234
chr16	11947773	11947879	E081	-8599
chr16	11948155	11948195	E081	-8283
chr16	11948383	11948423	E081	-8055
chr16	11948532	11948645	E081	-7833
chr16	11990563	11990629	E081	34085
chr16	12004836	12004880	E081	48358
chr16	12006332	12006427	E081	49854
chr16	11948383	11948423	E082	-8055
chr16	11948532	11948645	E082	-7833
chr16	12004736	12004822	E082	48258
chr16	12004836	12004880	E082	48358
chr16	12006332	12006427	E082	49854

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr16	11944358	11944403	E067	-12075
chr16	11944451	11944512	E067	-11966
chr16	11944528	11944669	E067	-11809
chr16	11944822	11946352	E067	-10126
chr16	11944358	11944403	E068	-12075
chr16	11944451	11944512	E068	-11966
chr16	11944528	11944669	E068	-11809
chr16	11944822	11946352	E068	-10126
chr16	11944358	11944403	E069	-12075
chr16	11944451	11944512	E069	-11966
chr16	11944528	11944669	E069	-11809
chr16	11944822	11946352	E069	-10126
chr16	11944358	11944403	E070	-12075
chr16	11944451	11944512	E070	-11966
chr16	11944528	11944669	E070	-11809
chr16	11944822	11946352	E070	-10126
chr16	11944358	11944403	E071	-12075
chr16	11944451	11944512	E071	-11966
chr16	11944528	11944669	E071	-11809
chr16	11944822	11946352	E071	-10126
chr16	11944358	11944403	E072	-12075
chr16	11944451	11944512	E072	-11966
chr16	11944528	11944669	E072	-11809
chr16	11944822	11946352	E072	-10126
chr16	11944358	11944403	E073	-12075
chr16	11944451	11944512	E073	-11966
chr16	11944528	11944669	E073	-11809
chr16	11944822	11946352	E073	-10126
chr16	11944358	11944403	E074	-12075
chr16	11944451	11944512	E074	-11966
chr16	11944528	11944669	E074	-11809
chr16	11944822	11946352	E074	-10126
chr16	11944358	11944403	E081	-12075
chr16	11944451	11944512	E081	-11966
chr16	11944528	11944669	E081	-11809
chr16	11944822	11946352	E081	-10126
chr16	11944358	11944403	E082	-12075
chr16	11944451	11944512	E082	-11966
chr16	11944528	11944669	E082	-11809
chr16	11944822	11946352	E082	-10126

rs154148

Genomic Coordinates

Gene: LOC105371084, uncharacterized LOC105371084(plus strand)

Population Frequency

P-Value

eQTL of rs154148 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs154148 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)