rs6519647

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

SEZ6L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0480 (14361/29880,GnomAD)
T=0488 (14219/29116,TOPMED)
G==0441 (2208/5008,1000G)
T=0435 (1676/3854,ALSPAC)
T=0452 (1677/3708,TWINSUK)

Position: chr22:26317998 (GRCh38.p7) (22q12.1)

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 22	NC_000022.11:g.26317998G>A
GRCh38.p7 chr 22	NC_000022.11:g.26317998G>T
GRCh37.p13 chr 22	NC_000022.10:g.26713964G>A
GRCh37.p13 chr 22	NC_000022.10:g.26713964G>T

Gene: SEZ6L, seizure related 6 homolog like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SEZ6L transcript variant 2	NM_001184773.1:c.	N/A	Intron Variant
SEZ6L transcript variant 3	NM_001184774.1:c.	N/A	Intron Variant
SEZ6L transcript variant 4	NM_001184775.1:c.	N/A	Intron Variant
SEZ6L transcript variant 5	NM_001184776.1:c.	N/A	Intron Variant
SEZ6L transcript variant 6	NM_001184777.1:c.	N/A	Intron Variant
SEZ6L transcript variant 1	NM_021115.4:c.	N/A	Intron Variant
SEZ6L transcript variant X2	XM_005261439.3:c.	N/A	Intron Variant
SEZ6L transcript variant X3	XM_005261440.3:c.	N/A	Intron Variant
SEZ6L transcript variant X1	XM_006724195.3:c.	N/A	Intron Variant
SEZ6L transcript variant X4	XM_011530037.2:c.	N/A	Intron Variant
SEZ6L transcript variant X6	XM_011530038.2:c.	N/A	Intron Variant
SEZ6L transcript variant X8	XM_011530039.2:c.	N/A	Intron Variant
SEZ6L transcript variant X5	XM_017028699.1:c.	N/A	Intron Variant
SEZ6L transcript variant X7	XM_017028700.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.443	T=0.557
1000Genomes	American	Sub	694	G=0.460	T=0.540
1000Genomes	East Asian	Sub	1008	G=0.471	T=0.529
1000Genomes	Europe	Sub	1006	G=0.530	T=0.470
1000Genomes	Global	Study-wide	5008	G=0.441	T=0.559
1000Genomes	South Asian	Sub	978	G=0.300	T=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.565	T=0.435
The Genome Aggregation Database	African	Sub	8698	G=0.444	A=0.000
The Genome Aggregation Database	American	Sub	836	G=0.510	A=0.00,
The Genome Aggregation Database	East Asian	Sub	1612	G=0.438	A=0.000
The Genome Aggregation Database	Europe	Sub	18432	G=0.562	A=0.000
The Genome Aggregation Database	Global	Study-wide	29880	G=0.519	A=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.520	A=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.511	T=0.488
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.548	T=0.452

PMID	Title	Author	Journal
23089632	A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.	Wang JC	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs6519647	1.33E-05	alcohol dependence	23089632

eQTL of rs6519647 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 rs6519647 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.