rs1550771

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC105373456 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0237 (7112/29966,GnomAD)
T==0269 (7843/29116,TOPMED)
T==0218 (1090/5008,1000G)
T==0183 (706/3854,ALSPAC)
T==0178 (661/3708,TWINSUK)

Position: chr2:18679109 (GRCh38.p7) (2p24.2)

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 2	NC_000002.12:g.18679109T>C
GRCh37.p13 chr 2	NC_000002.11:g.18860375T>C

Gene: LOC105373456, uncharacterized LOC105373456(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373456 transcript variant X8	XR_001739309.1:n....XR_001739309.1:n.764T>C	T>C	Non Coding Transcript Variant
LOC105373456 transcript variant X7	XR_001739308.1:n.	N/A	Intron Variant
LOC105373456 transcript variant X9	XR_001739310.1:n.	N/A	Intron Variant
LOC105373456 transcript variant X10	XR_001739311.1:n.	N/A	Intron Variant
LOC105373456 transcript variant X14	XR_001739312.1:n.	N/A	Intron Variant
LOC105373456 transcript variant X12	XR_939776.2:n.	N/A	Intron Variant
LOC105373456 transcript variant X1	XR_001739303.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X2	XR_001739304.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X4	XR_001739305.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X5	XR_001739306.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X6	XR_001739307.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X13	XR_001739313.1:n.	N/A	Genic Downstream Transcript Variant
LOC105373456 transcript variant X3	XR_427002.3:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.349	C=0.651
1000Genomes	American	Sub	694	T=0.270	C=0.730
1000Genomes	East Asian	Sub	1008	T=0.122	C=0.878
1000Genomes	Europe	Sub	1006	T=0.176	C=0.824
1000Genomes	Global	Study-wide	5008	T=0.218	C=0.782
1000Genomes	South Asian	Sub	978	T=0.150	C=0.850
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.183	C=0.817
The Genome Aggregation Database	African	Sub	8720	T=0.322	C=0.678
The Genome Aggregation Database	American	Sub	836	T=0.260	C=0.740
The Genome Aggregation Database	East Asian	Sub	1620	T=0.116	C=0.884
The Genome Aggregation Database	Europe	Sub	18488	T=0.206	C=0.793
The Genome Aggregation Database	Global	Study-wide	29966	T=0.237	C=0.762
The Genome Aggregation Database	Other	Sub	302	T=0.270	C=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.269	C=0.730
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.178	C=0.822

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
rs1550771	0.00054	alcohol dependence	20201924

eQTL of rs1550771 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 rs1550771 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.