SNP Detail Info-rs7424415

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLC39A10 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0301 (9038/29948,GnomAD)
T==0309 (9001/29118,TOPMED)
T==0393 (1967/5008,1000G)
T==0256 (988/3854,ALSPAC)
T==0245 (907/3708,TWINSUK)

Position: chr2:195671426 (GRCh38.p7) (2q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 27 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.195671426T>C
GRCh37.p13 chr 2	NC_000002.11:g.196536150T>C

Molecule type	Change	Amino acid[Codon]	SO Term
SLC39A10 transcript variant 1	NM_001127257.1:c.	N/A	Intron Variant
SLC39A10 transcript variant 2	NM_020342.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X1	XM_005246689.4:c.	N/A	Intron Variant
SLC39A10 transcript variant X2	XM_011511504.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X4	XM_011511505.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X5	XM_011511507.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X6	XM_017004522.1:c.	N/A	Intron Variant
SLC39A10 transcript variant X7	XM_017004523.1:c.	N/A	Intron Variant
SLC39A10 transcript variant X3	XM_011511506.2:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.266	C=0.734
1000Genomes	American	Sub	694	T=0.450	C=0.550
1000Genomes	East Asian	Sub	1008	T=0.586	C=0.414
1000Genomes	Europe	Sub	1006	T=0.266	C=0.734
1000Genomes	Global	Study-wide	5008	T=0.393	C=0.607
1000Genomes	South Asian	Sub	978	T=0.450	C=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.256	C=0.744
The Genome Aggregation Database	African	Sub	8718	T=0.279	C=0.721
The Genome Aggregation Database	American	Sub	836	T=0.450	C=0.550
The Genome Aggregation Database	East Asian	Sub	1620	T=0.623	C=0.377
The Genome Aggregation Database	Europe	Sub	18472	T=0.275	C=0.724
The Genome Aggregation Database	Global	Study-wide	29948	T=0.301	C=0.698
The Genome Aggregation Database	Other	Sub	302	T=0.430	C=0.570
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.309	C=0.690
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.245	C=0.755

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

SNP ID	p-value	Traits	Study
rs7424415	0.0001	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:196536150	SLC39A10	ENSG00000196950.9	T>C	9.2991e-9	95449	Cerebellum

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	196530924	196531064	E067	-5086
chr2	196531147	196531249	E067	-4901
chr2	196552291	196552796	E067	16141
chr2	196571743	196571934	E067	35593
chr2	196531147	196531249	E068	-4901
chr2	196551759	196551919	E068	15609
chr2	196552291	196552796	E068	16141
chr2	196532763	196532990	E069	-3160
chr2	196530924	196531064	E070	-5086
chr2	196531147	196531249	E070	-4901
chr2	196551398	196551453	E070	15248
chr2	196551579	196551657	E070	15429
chr2	196551759	196551919	E070	15609
chr2	196552291	196552796	E070	16141
chr2	196532763	196532990	E071	-3160
chr2	196552291	196552796	E071	16141
chr2	196530924	196531064	E073	-5086
chr2	196531147	196531249	E073	-4901
chr2	196530924	196531064	E074	-5086
chr2	196531147	196531249	E074	-4901
chr2	196526812	196526862	E081	-9288
chr2	196527010	196527154	E081	-8996
chr2	196527701	196527853	E081	-8297
chr2	196527862	196528001	E081	-8149
chr2	196528041	196528150	E081	-8000
chr2	196531147	196531249	E081	-4901
chr2	196552291	196552796	E082	16141

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	196520779	196524508	E067	-11642
chr2	196520779	196524508	E068	-11642
chr2	196520779	196524508	E069	-11642
chr2	196520779	196524508	E070	-11642
chr2	196520779	196524508	E071	-11642
chr2	196520779	196524508	E072	-11642
chr2	196520779	196524508	E073	-11642
chr2	196520779	196524508	E074	-11642
chr2	196520779	196524508	E081	-11642
chr2	196520779	196524508	E082	-11642

rs7424415