rs17042517

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0063 (1888/29982,GnomAD)
G=0062 (1805/29116,TOPMED)
G=0066 (333/5008,1000G)
G=0063 (243/3854,ALSPAC)
G=0064 (237/3708,TWINSUK)

Position: chr2:112882007 (GRCh38.p7) (2q14.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 67 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.112882007A>G
GRCh37.p13 chr 2	NC_000002.11:g.113639584A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.922	G=0.078
1000Genomes	American	Sub	694	A=0.970	G=0.030
1000Genomes	East Asian	Sub	1008	A=0.999	G=0.001
1000Genomes	Europe	Sub	1006	A=0.941	G=0.059
1000Genomes	Global	Study-wide	5008	A=0.934	G=0.066
1000Genomes	South Asian	Sub	978	A=0.850	G=0.150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.937	G=0.063
The Genome Aggregation Database	African	Sub	8726	A=0.920	G=0.080
The Genome Aggregation Database	American	Sub	838	A=0.950	G=0.050
The Genome Aggregation Database	East Asian	Sub	1622	A=1.000	G=0.000
The Genome Aggregation Database	Europe	Sub	18494	A=0.939	G=0.060
The Genome Aggregation Database	Global	Study-wide	29982	A=0.937	G=0.063
The Genome Aggregation Database	Other	Sub	302	A=0.910	G=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.938	G=0.062
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.936	G=0.064

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs17042517	0.000334	alcohol dependence	21314694

eQTL of rs17042517 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 rs17042517 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 )
chr2	113627573	113627734	E067	-11850
chr2	113628266	113628332	E067	-11252
chr2	113628413	113628487	E067	-11097
chr2	113628529	113628740	E067	-10844
chr2	113628899	113629083	E067	-10501
chr2	113638179	113638285	E067	-1299
chr2	113638319	113639332	E067	-252
chr2	113639552	113639674	E067	0
chr2	113628266	113628332	E068	-11252
chr2	113628413	113628487	E068	-11097
chr2	113628529	113628740	E068	-10844
chr2	113628899	113629083	E068	-10501
chr2	113637561	113638015	E068	-1569
chr2	113638179	113638285	E068	-1299
chr2	113638319	113639332	E068	-252
chr2	113639552	113639674	E068	0
chr2	113627573	113627734	E069	-11850
chr2	113628266	113628332	E069	-11252
chr2	113628413	113628487	E069	-11097
chr2	113628529	113628740	E069	-10844
chr2	113628899	113629083	E069	-10501
chr2	113629167	113629307	E069	-10277
chr2	113637561	113638015	E069	-1569
chr2	113638179	113638285	E069	-1299
chr2	113638319	113639332	E069	-252
chr2	113639552	113639674	E069	0
chr2	113627573	113627734	E070	-11850
chr2	113628413	113628487	E070	-11097
chr2	113628529	113628740	E070	-10844
chr2	113667975	113668032	E070	28391
chr2	113592037	113592255	E071	-47329
chr2	113626743	113627544	E071	-12040
chr2	113627573	113627734	E071	-11850
chr2	113628266	113628332	E071	-11252
chr2	113628413	113628487	E071	-11097
chr2	113628529	113628740	E071	-10844
chr2	113628899	113629083	E071	-10501
chr2	113637145	113637296	E071	-2288
chr2	113637561	113638015	E071	-1569
chr2	113638179	113638285	E071	-1299
chr2	113638319	113639332	E071	-252
chr2	113639552	113639674	E071	0
chr2	113680696	113681114	E071	41112
chr2	113681388	113681438	E071	41804
chr2	113626743	113627544	E072	-12040
chr2	113627573	113627734	E072	-11850
chr2	113628266	113628332	E072	-11252
chr2	113638179	113638285	E072	-1299
chr2	113638319	113639332	E072	-252
chr2	113639552	113639674	E072	0
chr2	113647758	113647880	E072	8174
chr2	113628529	113628740	E073	-10844
chr2	113628899	113629083	E073	-10501
chr2	113629167	113629307	E073	-10277
chr2	113637561	113638015	E073	-1569
chr2	113638179	113638285	E073	-1299
chr2	113638319	113639332	E073	-252
chr2	113626743	113627544	E074	-12040
chr2	113627573	113627734	E074	-11850
chr2	113628266	113628332	E074	-11252
chr2	113628413	113628487	E074	-11097
chr2	113628529	113628740	E074	-10844
chr2	113628899	113629083	E074	-10501
chr2	113629167	113629307	E074	-10277
chr2	113638179	113638285	E074	-1299
chr2	113638319	113639332	E074	-252
chr2	113639552	113639674	E074	0