rs6927244

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105374928 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0014 (422/29976,GnomAD)
A=0017 (517/29118,TOPMED)
A=0013 (65/5008,1000G)

Position: chr6:11510625 (GRCh38.p7) (6p24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 52 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.11510625G>A
GRCh37.p13 chr 6	NC_000006.11:g.11510858G>A

Gene: LOC105374928, uncharacterized LOC105374928(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374928 transcript variant X1	XR_926478.2:n.	N/A	Intron Variant
LOC105374928 transcript variant X3	XR_926482.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.955	A=0.045
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.987	A=0.013
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Genome Aggregation Database	African	Sub	8728	G=0.953	A=0.047
The Genome Aggregation Database	American	Sub	836	G=1.000	A=0.000
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18490	G=0.999	A=0.000
The Genome Aggregation Database	Global	Study-wide	29976	G=0.985	A=0.014
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.982	A=0.017

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
rs6927244	0.0004	alcohol dependence	21314694

eQTL of rs6927244 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 rs6927244 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 )
chr6	11495044	11495323	E067	-15535
chr6	11495583	11495726	E067	-15132
chr6	11495836	11495986	E067	-14872
chr6	11496061	11496115	E067	-14743
chr6	11552726	11552933	E067	41868
chr6	11485636	11485747	E068	-25111
chr6	11495044	11495323	E068	-15535
chr6	11496061	11496115	E068	-14743
chr6	11536030	11536493	E068	25172
chr6	11536774	11536825	E068	25916
chr6	11536867	11536941	E068	26009
chr6	11544879	11544987	E068	34021
chr6	11551304	11551398	E068	40446
chr6	11551558	11551641	E068	40700
chr6	11551968	11552070	E068	41110
chr6	11485636	11485747	E069	-25111
chr6	11551968	11552070	E069	41110
chr6	11552726	11552933	E069	41868
chr6	11485636	11485747	E070	-25111
chr6	11486230	11486310	E070	-24548
chr6	11486401	11487037	E070	-23821
chr6	11544879	11544987	E070	34021
chr6	11552726	11552933	E070	41868
chr6	11485636	11485747	E071	-25111
chr6	11486230	11486310	E071	-24548
chr6	11495044	11495323	E071	-15535
chr6	11536030	11536493	E071	25172
chr6	11536774	11536825	E071	25916
chr6	11552726	11552933	E071	41868
chr6	11485636	11485747	E072	-25111
chr6	11496207	11497212	E072	-13646
chr6	11551304	11551398	E072	40446
chr6	11551558	11551641	E072	40700
chr6	11552726	11552933	E072	41868
chr6	11473275	11473597	E073	-37261
chr6	11495044	11495323	E073	-15535
chr6	11495583	11495726	E073	-15132
chr6	11495836	11495986	E073	-14872
chr6	11496061	11496115	E073	-14743
chr6	11496207	11497212	E073	-13646
chr6	11484754	11484972	E074	-25886
chr6	11485636	11485747	E074	-25111
chr6	11486230	11486310	E074	-24548
chr6	11551304	11551398	E074	40446
chr6	11551558	11551641	E074	40700
chr6	11551968	11552070	E074	41110
chr6	11552726	11552933	E074	41868
chr6	11556546	11556638	E074	45688
chr6	11556659	11556863	E074	45801
chr6	11536774	11536825	E082	25916
chr6	11536867	11536941	E082	26009
chr6	11544879	11544987	E082	34021

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	11536964	11539273	E067	26106
chr6	11539795	11539848	E067	28937
chr6	11536964	11539273	E068	26106
chr6	11539795	11539848	E068	28937
chr6	11536964	11539273	E069	26106
chr6	11539795	11539848	E069	28937
chr6	11536964	11539273	E070	26106
chr6	11539795	11539848	E070	28937
chr6	11536964	11539273	E071	26106
chr6	11539795	11539848	E071	28937
chr6	11536964	11539273	E072	26106
chr6	11539795	11539848	E072	28937
chr6	11536964	11539273	E073	26106
chr6	11539795	11539848	E073	28937
chr6	11536964	11539273	E074	26106
chr6	11536964	11539273	E081	26106
chr6	11539795	11539848	E081	28937
chr6	11536964	11539273	E082	26106
chr6	11539795	11539848	E082	28937