SNP Detail Info-rs10864699

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

GALNT2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0276 (8285/29944,GnomAD)
A=0304 (8867/29116,TOPMED)
A=0260 (1304/5008,1000G)
A=0287 (1107/3854,ALSPAC)
A=0273 (1014/3708,TWINSUK)

Position: chr1:230128860 (GRCh38.p7) (1q42.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 22 Enhancers around

Promoter: 2 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
GALNT2 transcript variant 2	NM_001291866.1:c.	N/A	Intron Variant
GALNT2 transcript variant 1	NM_004481.4:c.	N/A	Intron Variant
GALNT2 transcript variant 3	NR_120373.1:n.	N/A	Genic Downstream Transcript Variant
GALNT2 transcript variant X1	XM_017000963.1:c.	N/A	Intron Variant
GALNT2 transcript variant X2	XM_017000964.1:c.	N/A	Intron Variant
GALNT2 transcript variant X3	XM_017000965.1:c.	N/A	Intron Variant
GALNT2 transcript variant X4	XM_017000966.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.660	A=0.340
1000Genomes	American	Sub	694	G=0.780	A=0.220
1000Genomes	East Asian	Sub	1008	G=0.760	A=0.240
1000Genomes	Europe	Sub	1006	G=0.750	A=0.250
1000Genomes	Global	Study-wide	5008	G=0.740	A=0.260
1000Genomes	South Asian	Sub	978	G=0.790	A=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.713	A=0.287
The Genome Aggregation Database	African	Sub	8710	G=0.683	A=0.317
The Genome Aggregation Database	American	Sub	836	G=0.790	A=0.21,
The Genome Aggregation Database	East Asian	Sub	1618	G=0.778	A=0.222
The Genome Aggregation Database	Europe	Sub	18478	G=0.734	A=0.265
The Genome Aggregation Database	Global	Study-wide	29944	G=0.723	A=0.276
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.24,
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.695	A=0.304
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.727	A=0.273

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs10864699	0.000183	alcohol consumption	23743675

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	101265148	101265394	E067	-21591
chr1	101265556	101266024	E067	-20961
chr1	101265148	101265394	E068	-21591
chr1	101265556	101266024	E068	-20961
chr1	101331748	101331921	E068	44763
chr1	101265148	101265394	E069	-21591
chr1	101265556	101266024	E069	-20961
chr1	101265148	101265394	E071	-21591
chr1	101265556	101266024	E071	-20961
chr1	101251157	101251669	E072	-35316
chr1	101265148	101265394	E072	-21591
chr1	101265556	101266024	E072	-20961
chr1	101312534	101312656	E072	25549
chr1	101265148	101265394	E074	-21591
chr1	101265556	101266024	E074	-20961
chr1	101260280	101261531	E081	-25454
chr1	101261730	101261869	E081	-25116
chr1	101261920	101262012	E081	-24973
chr1	101262183	101262259	E081	-24726
chr1	101272190	101272543	E081	-14442
chr1	101299905	101300209	E081	12920
chr1	101300348	101301767	E081	13363

rs10864699

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	101313044	101313362	E068	26059
chr1	101313044	101313362	E071	26059