rs4971371

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SNTG2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0440 (13151/29850,GnomAD)
C==0478 (13924/29116,TOPMED)
C==0453 (2267/5008,1000G)
C==0383 (1477/3854,ALSPAC)
C==0392 (1453/3708,TWINSUK)

Position: chr2:1080998 (GRCh38.p7) (2p25.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 12 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.1080998C>T
GRCh37.p13 chr 2	NC_000002.11:g.1076684C>T

Gene: SNTG2, syntrophin gamma 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNTG2 transcript	NM_018968.3:c.	N/A	Intron Variant
SNTG2 transcript variant X8	XM_011510366.2:c.	N/A	Intron Variant
SNTG2 transcript variant X1	XM_017004361.1:c.	N/A	Intron Variant
SNTG2 transcript variant X2	XM_017004362.1:c.	N/A	Intron Variant
SNTG2 transcript variant X3	XM_017004363.1:c.	N/A	Intron Variant
SNTG2 transcript variant X5	XM_017004365.1:c.	N/A	Intron Variant
SNTG2 transcript variant X6	XM_017004366.1:c.	N/A	Intron Variant
SNTG2 transcript variant X7	XM_017004367.1:c.	N/A	Intron Variant
SNTG2 transcript variant X9	XM_017004368.1:c.	N/A	Intron Variant
SNTG2 transcript variant X10	XM_017004369.1:c.	N/A	Intron Variant
SNTG2 transcript variant X11	XM_017004370.1:c.	N/A	Intron Variant
SNTG2 transcript variant X12	XM_017004371.1:c.	N/A	Intron Variant
SNTG2 transcript variant X13	XM_017004372.1:c.	N/A	Intron Variant
SNTG2 transcript variant X16	XM_017004374.1:c.	N/A	Intron Variant
SNTG2 transcript variant X4	XM_017004364.1:c.	N/A	Genic Upstream Transcript Variant
SNTG2 transcript variant X14	XM_017004373.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.573	T=0.427
1000Genomes	American	Sub	694	C=0.410	T=0.590
1000Genomes	East Asian	Sub	1008	C=0.356	T=0.644
1000Genomes	Europe	Sub	1006	C=0.385	T=0.615
1000Genomes	Global	Study-wide	5008	C=0.453	T=0.547
1000Genomes	South Asian	Sub	978	C=0.490	T=0.510
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.383	T=0.617
The Genome Aggregation Database	African	Sub	8694	C=0.545	T=0.455
The Genome Aggregation Database	American	Sub	836	C=0.380	T=0.620
The Genome Aggregation Database	East Asian	Sub	1614	C=0.376	T=0.624
The Genome Aggregation Database	Europe	Sub	18406	C=0.399	T=0.600
The Genome Aggregation Database	Global	Study-wide	29850	C=0.440	T=0.559
The Genome Aggregation Database	Other	Sub	300	C=0.470	T=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.478	T=0.521
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.392	T=0.608

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

P-Value

SNP ID	p-value	Traits	Study
rs4971371	0.000557	alcohol dependence	21314694

eQTL of rs4971371 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 rs4971371 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	1077535	1077722	E070	851
chr2	1077762	1077880	E070	1078
chr2	1077535	1077722	E072	851
chr2	1077762	1077880	E072	1078
chr2	1032807	1032940	E081	-43744
chr2	1032990	1033107	E081	-43577
chr2	1033203	1033413	E081	-43271
chr2	1077535	1077722	E081	851
chr2	1077762	1077880	E081	1078
chr2	1124227	1124368	E081	47543
chr2	1032807	1032940	E082	-43744
chr2	1032990	1033107	E082	-43577