rs488109

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

LOC105373262 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0272 (8106/29804,GnomAD)
C==0361 (10529/29116,TOPMED)
C==0415 (2080/5008,1000G)
C==0044 (169/3854,ALSPAC)
C==0041 (153/3708,TWINSUK)

Position: chr1:244265229 (GRCh38.p7) (1q44)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 49 Enhancers around

Promoter: 23 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.244265229C>G
GRCh37.p13 chr 1	NC_000001.10:g.244428531C>G

Gene: LOC105373262, uncharacterized LOC105373262(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373262 transcript variant X2	XR_001738564.1:n.	N/A	Intron Variant
LOC105373262 transcript variant X5	XR_001738565.1:n.	N/A	Intron Variant
LOC105373262 transcript variant X3	XR_949343.2:n.	N/A	Intron Variant
LOC105373262 transcript variant X4	XR_949344.2:n.	N/A	Genic Upstream Transcript Variant
LOC105373262 transcript variant X1	XR_001738563.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.815	G=0.185
1000Genomes	American	Sub	694	C=0.370	G=0.630
1000Genomes	East Asian	Sub	1008	C=0.457	G=0.543
1000Genomes	Europe	Sub	1006	C=0.065	G=0.935
1000Genomes	Global	Study-wide	5008	C=0.415	G=0.585
1000Genomes	South Asian	Sub	978	C=0.220	G=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.044	G=0.956
The Genome Aggregation Database	African	Sub	8636	C=0.700	G=0.300
The Genome Aggregation Database	American	Sub	832	C=0.350	G=0.650
The Genome Aggregation Database	East Asian	Sub	1572	C=0.461	G=0.539
The Genome Aggregation Database	Europe	Sub	18462	C=0.055	G=0.944
The Genome Aggregation Database	Global	Study-wide	29804	C=0.272	G=0.728
The Genome Aggregation Database	Other	Sub	302	C=0.060	G=0.940
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.361	G=0.638
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.041	G=0.959

PMID	Title	Author	Journal
29071344	Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.	Zhou H	JAMA Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs488109	4E-06	alcohol dependence	29071344

eQTL of rs488109 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 rs488109 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	244381054	244381104	E067	-47427
chr1	244394542	244394697	E067	-33834
chr1	244435614	244437888	E067	7083
chr1	244381054	244381104	E068	-47427
chr1	244381559	244381943	E068	-46588
chr1	244435486	244435595	E068	6955
chr1	244435614	244437888	E068	7083
chr1	244466897	244466959	E068	38366
chr1	244475136	244475346	E068	46605
chr1	244475466	244475828	E068	46935
chr1	244381054	244381104	E069	-47427
chr1	244394542	244394697	E069	-33834
chr1	244435126	244435225	E069	6595
chr1	244435486	244435595	E069	6955
chr1	244435614	244437888	E069	7083
chr1	244381559	244381943	E070	-46588
chr1	244394542	244394697	E070	-33834
chr1	244435486	244435595	E070	6955
chr1	244435614	244437888	E070	7083
chr1	244381054	244381104	E071	-47427
chr1	244435486	244435595	E071	6955
chr1	244435614	244437888	E071	7083
chr1	244460883	244460969	E071	32352
chr1	244461028	244461235	E071	32497
chr1	244461409	244461459	E071	32878
chr1	244475466	244475828	E071	46935
chr1	244381054	244381104	E072	-47427
chr1	244381559	244381943	E072	-46588
chr1	244435486	244435595	E072	6955
chr1	244435614	244437888	E072	7083
chr1	244381054	244381104	E073	-47427
chr1	244381559	244381943	E073	-46588
chr1	244435486	244435595	E073	6955
chr1	244435614	244437888	E073	7083
chr1	244381054	244381104	E074	-47427
chr1	244394542	244394697	E074	-33834
chr1	244435486	244435595	E074	6955
chr1	244435614	244437888	E074	7083
chr1	244475466	244475828	E074	46935
chr1	244408382	244408478	E081	-20053
chr1	244434997	244435091	E081	6466
chr1	244435126	244435225	E081	6595
chr1	244435486	244435595	E081	6955
chr1	244466141	244466824	E081	37610
chr1	244466897	244466959	E081	38366
chr1	244394542	244394697	E082	-33834
chr1	244434997	244435091	E082	6466
chr1	244435126	244435225	E082	6595
chr1	244435614	244437888	E082	7083

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	244394753	244395493	E067	-33038
chr1	244462517	244463185	E067	33986
chr1	244463192	244463263	E067	34661
chr1	244394753	244395493	E068	-33038
chr1	244462517	244463185	E068	33986
chr1	244463192	244463263	E068	34661
chr1	244394753	244395493	E069	-33038
chr1	244462517	244463185	E069	33986
chr1	244463192	244463263	E069	34661
chr1	244394753	244395493	E071	-33038
chr1	244462517	244463185	E071	33986
chr1	244463192	244463263	E071	34661
chr1	244394753	244395493	E072	-33038
chr1	244462517	244463185	E072	33986
chr1	244463192	244463263	E072	34661
chr1	244394753	244395493	E073	-33038
chr1	244462517	244463185	E073	33986
chr1	244463192	244463263	E073	34661
chr1	244394753	244395493	E074	-33038
chr1	244462517	244463185	E074	33986
chr1	244394753	244395493	E082	-33038
chr1	244462517	244463185	E082	33986
chr1	244463192	244463263	E082	34661