rs2179556

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC105374972 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0202 (6051/29936,GnomAD)
T==0157 (4572/29118,TOPMED)
T==0198 (994/5008,1000G)
T==0229 (884/3854,ALSPAC)
T==0241 (895/3708,TWINSUK)

Position: chr6:22689022 (GRCh38.p7) (6p22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 63 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.22689022T>C
GRCh37.p13 chr 6	NC_000006.11:g.22689251T>C

Gene: LOC105374972, uncharacterized LOC105374972(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374972 transcript variant 1	NR_134613.1:n.	N/A	Intron Variant
LOC105374972 transcript variant 2	NR_134614.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.076	C=0.924
1000Genomes	American	Sub	694	T=0.150	C=0.850
1000Genomes	East Asian	Sub	1008	T=0.361	C=0.639
1000Genomes	Europe	Sub	1006	T=0.242	C=0.758
1000Genomes	Global	Study-wide	5008	T=0.198	C=0.802
1000Genomes	South Asian	Sub	978	T=0.190	C=0.810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.229	C=0.771
The Genome Aggregation Database	African	Sub	8716	T=0.099	C=0.901
The Genome Aggregation Database	American	Sub	838	T=0.120	C=0.880
The Genome Aggregation Database	East Asian	Sub	1618	T=0.339	C=0.661
The Genome Aggregation Database	Europe	Sub	18462	T=0.241	C=0.758
The Genome Aggregation Database	Global	Study-wide	29936	T=0.202	C=0.797
The Genome Aggregation Database	Other	Sub	302	T=0.250	C=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.157	C=0.843
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.241	C=0.759

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs2179556	0.00091	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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	22654945	22655093	E067	-34158
chr6	22656798	22658987	E067	-30264
chr6	22659075	22659601	E067	-29650
chr6	22654945	22655093	E068	-34158
chr6	22656798	22658987	E068	-30264
chr6	22659075	22659601	E068	-29650
chr6	22660313	22660363	E068	-28888
chr6	22660486	22660557	E068	-28694
chr6	22698811	22698889	E068	9560
chr6	22699155	22699205	E068	9904
chr6	22699417	22699914	E068	10166
chr6	22709122	22709352	E068	19871
chr6	22710016	22711317	E068	20765
chr6	22718223	22718398	E068	28972
chr6	22654068	22654800	E069	-34451
chr6	22656798	22658987	E069	-30264
chr6	22659075	22659601	E069	-29650
chr6	22699417	22699914	E069	10166
chr6	22710016	22711317	E069	20765
chr6	22737189	22737464	E069	47938
chr6	22647728	22647778	E070	-41473
chr6	22648047	22648214	E070	-41037
chr6	22656538	22656614	E070	-32637
chr6	22656619	22656753	E070	-32498
chr6	22656798	22658987	E070	-30264
chr6	22659075	22659601	E070	-29650
chr6	22660313	22660363	E070	-28888
chr6	22660486	22660557	E070	-28694
chr6	22660659	22660750	E070	-28501
chr6	22696838	22696945	E070	7587
chr6	22697634	22697704	E070	8383
chr6	22699155	22699205	E070	9904
chr6	22699417	22699914	E070	10166
chr6	22737533	22737990	E070	48282
chr6	22654068	22654800	E071	-34451
chr6	22654945	22655093	E071	-34158
chr6	22656798	22658987	E071	-30264
chr6	22659075	22659601	E071	-29650
chr6	22698811	22698889	E071	9560
chr6	22699155	22699205	E071	9904
chr6	22699417	22699914	E071	10166
chr6	22710016	22711317	E071	20765
chr6	22652118	22652214	E072	-37037
chr6	22654068	22654800	E072	-34451
chr6	22654945	22655093	E072	-34158
chr6	22659075	22659601	E072	-29650
chr6	22699155	22699205	E072	9904
chr6	22656143	22656203	E074	-33048
chr6	22656538	22656614	E074	-32637
chr6	22656619	22656753	E074	-32498
chr6	22656798	22658987	E074	-30264
chr6	22659075	22659601	E074	-29650
chr6	22710016	22711317	E074	20765
chr6	22718223	22718398	E074	28972
chr6	22659075	22659601	E081	-29650
chr6	22660313	22660363	E081	-28888
chr6	22660486	22660557	E081	-28694
chr6	22660659	22660750	E081	-28501
chr6	22668850	22669547	E081	-19704
chr6	22656798	22658987	E082	-30264
chr6	22659075	22659601	E082	-29650
chr6	22710016	22711317	E082	20765
chr6	22718223	22718398	E082	28972

rs2179556

Genomic Coordinates

Gene: LOC105374972, uncharacterized LOC105374972(minus strand)

Population Frequency

P-Value

eQTL of rs2179556 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2179556 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)