rs1412787

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC105371609 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0263 (7867/29910,GnomAD)
T=0222 (6463/29118,TOPMED)
T=0272 (1362/5008,1000G)
T=0309 (1190/3854,ALSPAC)
T=0315 (1167/3708,TWINSUK)

Position: chr1:170239583 (GRCh38.p7) (1q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.170239583C>T
GRCh37.p13 chr 1	NC_000001.10:g.170208724C>T

Gene: LOC105371609, uncharacterized LOC105371609(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371609 transcript variant X1	XR_001738284.1:n....XR_001738284.1:n.2625C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X2	XR_922266.2:n.262...XR_922266.2:n.2625C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X3	XR_001738285.1:n....XR_001738285.1:n.2453C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X4	XR_001738286.1:n....XR_001738286.1:n.2625C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X5	XR_001738287.1:n....XR_001738287.1:n.1670C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X6	XR_922269.2:n.262...XR_922269.2:n.2625C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X7	XR_001738288.1:n....XR_001738288.1:n.2625C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X8	XR_001738289.1:n....XR_001738289.1:n.3073C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X10	XR_001738290.1:n....XR_001738290.1:n.2615C>T	C>T	Non Coding Transcript Variant
LOC105371609 transcript variant X9	XR_922275.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.930	T=0.070
1000Genomes	American	Sub	694	C=0.780	T=0.220
1000Genomes	East Asian	Sub	1008	C=0.562	T=0.438
1000Genomes	Europe	Sub	1006	C=0.675	T=0.325
1000Genomes	Global	Study-wide	5008	C=0.728	T=0.272
1000Genomes	South Asian	Sub	978	C=0.650	T=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.691	T=0.309
The Genome Aggregation Database	African	Sub	8714	C=0.901	T=0.099
The Genome Aggregation Database	American	Sub	832	C=0.760	T=0.240
The Genome Aggregation Database	East Asian	Sub	1598	C=0.559	T=0.441
The Genome Aggregation Database	Europe	Sub	18464	C=0.674	T=0.325
The Genome Aggregation Database	Global	Study-wide	29910	C=0.737	T=0.263
The Genome Aggregation Database	Other	Sub	302	C=0.700	T=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.778	T=0.222
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.685	T=0.315

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

P-Value

SNP ID	p-value	Traits	Study
rs1412787	0.00041	alcohol dependence	20201924

eQTL of rs1412787 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 rs1412787 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.