rs1322416

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

LGSN : Intron Variant
PTP4A1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0470 (14072/29910,GnomAD)
T==0394 (11482/29118,TOPMED)
T==0432 (2165/5008,1000G)
G=0450 (1733/3854,ALSPAC)
G=0453 (1680/3708,TWINSUK)

Position: chr6:63544114 (GRCh38.p7) (6q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.63544114T>G
GRCh37.p13 chr 6	NC_000006.11:g.64254019T>G

Gene: LGSN, lengsin, lens protein with glutamine synthetase domain(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LGSN transcript variant 2	NM_001143940.1:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant 1	NM_016571.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X1	XM_017010929.1:c.	N/A	Intron Variant
LGSN transcript variant X2	XM_011535889.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X4	XM_011535892.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X3	XM_017010930.1:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X5	XM_017010931.1:c.	N/A	Genic Upstream Transcript Variant

Gene: PTP4A1, protein tyrosine phosphatase type IVA, member 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTP4A1 transcript	NM_003463.4:c.	N/A	Genic Upstream Transcript Variant
PTP4A1 transcript variant X1	XM_017011270.1:c.	N/A	Intron Variant
PTP4A1 transcript variant X4	XM_011536111.1:c.	N/A	Genic Upstream Transcript Variant
PTP4A1 transcript variant X3	XM_011536112.1:c.	N/A	Genic Upstream Transcript Variant
PTP4A1 transcript variant X2	XM_017011271.1:c.	N/A	Genic Upstream Transcript Variant
PTP4A1 transcript variant X5	XM_017011272.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.202	G=0.798
1000Genomes	American	Sub	694	T=0.420	G=0.580
1000Genomes	East Asian	Sub	1008	T=0.551	G=0.449
1000Genomes	Europe	Sub	1006	T=0.581	G=0.419
1000Genomes	Global	Study-wide	5008	T=0.432	G=0.568
1000Genomes	South Asian	Sub	978	T=0.480	G=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.550	G=0.450
The Genome Aggregation Database	African	Sub	8696	T=0.231	G=0.769
The Genome Aggregation Database	American	Sub	838	T=0.420	G=0.580
The Genome Aggregation Database	East Asian	Sub	1616	T=0.551	G=0.449
The Genome Aggregation Database	Europe	Sub	18460	T=0.575	G=0.424
The Genome Aggregation Database	Global	Study-wide	29910	T=0.470	G=0.529
The Genome Aggregation Database	Other	Sub	300	T=0.630	G=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.394	G=0.605
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.547	G=0.453

PMID	Title	Author	Journal
22096494	A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.	Zuo L	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs1322416	7.5E-06	alcohol dependence	22096494

eQTL of rs1322416 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr6:64254019	LGSN	ENSG00000146166.12	T>G	1.9599e-12	224137	Brain_Spinal_cord_cervical

meQTL of rs1322416 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	64280974	64281053	E068	26955
chr6	64299831	64300142	E069	45812
chr6	64286353	64286524	E070	32334
chr6	64286353	64286524	E071	32334
chr6	64295649	64295699	E071	41630
chr6	64263119	64263520	E081	9100
chr6	64263943	64264222	E081	9924
chr6	64286353	64286524	E081	32334
chr6	64286849	64286961	E081	32830

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	64281208	64284581	E067	27189
chr6	64281208	64284581	E068	27189
chr6	64281208	64284581	E069	27189
chr6	64281208	64284581	E070	27189
chr6	64281208	64284581	E071	27189
chr6	64281208	64284581	E072	27189
chr6	64281208	64284581	E073	27189
chr6	64281208	64284581	E074	27189
chr6	64281208	64284581	E081	27189
chr6	64281208	64284581	E082	27189