SNP Detail Info-rs12562911

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ST6GALNAC3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0267 (8001/29884,GnomAD)
G=0243 (7094/29118,TOPMED)
G=0369 (1847/5008,1000G)
G=0269 (1036/3854,ALSPAC)
G=0260 (965/3708,TWINSUK)

Position: chr1:76356915 (GRCh38.p7) (1p31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 40 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.76356915A>G
GRCh37.p13 chr 1	NC_000001.10:g.76822600A>G

Molecule type	Change	Amino acid[Codon]	SO Term
ST6GALNAC3 transcript variant 2	NM_001160011.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant 1	NM_152996.2:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X2	XM_006710553.3:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X1	XM_017000937.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X2	XM_017000938.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X3	XM_017000939.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X5	XM_017000940.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X6	XM_017000941.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X7	XM_017000942.1:c.	N/A	Intron Variant
ST6GALNAC3 transcript variant X8	XR_001737093.1:n.	N/A	Intron Variant
ST6GALNAC3 transcript variant X9	XR_001737094.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.790	G=0.210
1000Genomes	American	Sub	694	A=0.770	G=0.230
1000Genomes	East Asian	Sub	1008	A=0.359	G=0.641
1000Genomes	Europe	Sub	1006	A=0.766	G=0.234
1000Genomes	Global	Study-wide	5008	A=0.631	G=0.369
1000Genomes	South Asian	Sub	978	A=0.460	G=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.731	G=0.269
The Genome Aggregation Database	African	Sub	8690	A=0.796	G=0.204
The Genome Aggregation Database	American	Sub	836	A=0.780	G=0.220
The Genome Aggregation Database	East Asian	Sub	1616	A=0.344	G=0.656
The Genome Aggregation Database	Europe	Sub	18440	A=0.734	G=0.265
The Genome Aggregation Database	Global	Study-wide	29884	A=0.732	G=0.267
The Genome Aggregation Database	Other	Sub	302	A=0.680	G=0.320
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.756	G=0.243
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.740	G=0.260

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs12562911	0.000762	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	76796627	76796734	E067	-25866
chr1	76796738	76797021	E067	-25579
chr1	76802549	76803148	E067	-19452
chr1	76803380	76803463	E067	-19137
chr1	76803651	76803756	E067	-18844
chr1	76796627	76796734	E068	-25866
chr1	76796738	76797021	E068	-25579
chr1	76803380	76803463	E068	-19137
chr1	76858239	76858398	E068	35639
chr1	76796627	76796734	E069	-25866
chr1	76796738	76797021	E069	-25579
chr1	76803380	76803463	E069	-19137
chr1	76803651	76803756	E069	-18844
chr1	76817888	76818044	E069	-4556
chr1	76818083	76818163	E069	-4437
chr1	76857754	76857804	E070	35154
chr1	76858239	76858398	E070	35639
chr1	76796627	76796734	E071	-25866
chr1	76796738	76797021	E071	-25579
chr1	76803651	76803756	E071	-18844
chr1	76796627	76796734	E072	-25866
chr1	76796738	76797021	E072	-25579
chr1	76803380	76803463	E072	-19137
chr1	76803651	76803756	E072	-18844
chr1	76831864	76831953	E072	9264
chr1	76857754	76857804	E072	35154
chr1	76831864	76831953	E073	9264
chr1	76832360	76832904	E073	9760
chr1	76796627	76796734	E074	-25866
chr1	76796738	76797021	E074	-25579
chr1	76801801	76801870	E074	-20730
chr1	76801939	76801989	E074	-20611
chr1	76802549	76803148	E074	-19452
chr1	76803380	76803463	E074	-19137
chr1	76803651	76803756	E074	-18844
chr1	76817888	76818044	E074	-4556
chr1	76858239	76858398	E074	35639
chr1	76821112	76821627	E081	-973
chr1	76856161	76856476	E081	33561
chr1	76857754	76857804	E081	35154

rs12562911