SNP Detail Info-rs6756374

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

SLC39A10 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0281 (8427/29926,GnomAD)
C==0291 (8499/29118,TOPMED)
C==0325 (1629/5008,1000G)
C==0255 (982/3854,ALSPAC)
C==0242 (899/3708,TWINSUK)

Position: chr2:195722946 (GRCh38.p7) (2q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.195722946C>A
GRCh37.p13 chr 2	NC_000002.11:g.196587670C>A

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 X3	XM_011511506.2: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	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.265	A=0.735
1000Genomes	American	Sub	694	C=0.380	A=0.620
1000Genomes	East Asian	Sub	1008	C=0.319	A=0.681
1000Genomes	Europe	Sub	1006	C=0.265	A=0.735
1000Genomes	Global	Study-wide	5008	C=0.325	A=0.675
1000Genomes	South Asian	Sub	978	C=0.430	A=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.255	A=0.745
The Genome Aggregation Database	African	Sub	8704	C=0.276	A=0.724
The Genome Aggregation Database	American	Sub	838	C=0.360	A=0.640
The Genome Aggregation Database	East Asian	Sub	1616	C=0.349	A=0.651
The Genome Aggregation Database	Europe	Sub	18468	C=0.272	A=0.727
The Genome Aggregation Database	Global	Study-wide	29926	C=0.281	A=0.718
The Genome Aggregation Database	Other	Sub	300	C=0.420	A=0.580
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.291	A=0.708
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.242	A=0.758

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
rs6756374	0.00011	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:196587670	SLC39A10	ENSG00000196950.9	C>A	9.2991e-9	146969	Cerebellum

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	196552291	196552796	E067	-34874
chr2	196571743	196571934	E067	-15736
chr2	196551759	196551919	E068	-35751
chr2	196552291	196552796	E068	-34874
chr2	196551398	196551453	E070	-36217
chr2	196551579	196551657	E070	-36013
chr2	196551759	196551919	E070	-35751
chr2	196552291	196552796	E070	-34874
chr2	196552291	196552796	E071	-34874
chr2	196552291	196552796	E082	-34874

rs6756374