rs17620991

Organism: Homo sapiens

Alleles: G>C / G>T

Gene : Feature

SUGCT : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0119 (3575/29980,GnomAD)
C=0107 (535/5008,1000G)
C=0145 (559/3854,ALSPAC)
C=0155 (573/3708,TWINSUK)

Position: chr7:40796922 (GRCh38.p7) (7p14.1)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 8 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.40796922G>C
GRCh38.p7 chr 7	NC_000007.14:g.40796922G>T
GRCh37.p13 chr 7	NC_000007.13:g.40836521G>C
GRCh37.p13 chr 7	NC_000007.13:g.40836521G>T
SUGCT RefSeqGene	NG_023422.1:g.666947G>C
SUGCT RefSeqGene	NG_023422.1:g.666947G>T

Gene: SUGCT, succinyl-CoA:glutarate-CoA transferase(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SUGCT transcript variant 1	NM_001193311.1:c.	N/A	Intron Variant
SUGCT transcript variant 2	NM_001193312.1:c.	N/A	Intron Variant
SUGCT transcript variant 3	NM_001193313.1:c.	N/A	Intron Variant
SUGCT transcript variant 4	NM_024728.2:c.	N/A	Intron Variant
SUGCT transcript variant X2	XM_006715775.3:c.	N/A	Intron Variant
SUGCT transcript variant X1	XM_011515525.2:c.	N/A	Intron Variant
SUGCT transcript variant X3	XM_011515526.2:c.	N/A	Intron Variant
SUGCT transcript variant X5	XM_011515527.2:c.	N/A	Intron Variant
SUGCT transcript variant X8	XM_011515529.2:c.	N/A	Intron Variant
SUGCT transcript variant X4	XM_017012621.1:c.	N/A	Intron Variant
SUGCT transcript variant X7	XM_011515528.2:c.	N/A	Genic Downstream Transcript Variant
SUGCT transcript variant X9	XM_011515530.2:c.	N/A	Genic Downstream Transcript Variant
SUGCT transcript variant X6	XM_017012622.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.992	C=0.008
1000Genomes	American	Sub	694	G=0.860	C=0.140
1000Genomes	East Asian	Sub	1008	G=0.976	C=0.024
1000Genomes	Europe	Sub	1006	G=0.850	C=0.150
1000Genomes	Global	Study-wide	5008	G=0.893	C=0.107
1000Genomes	South Asian	Sub	978	G=0.740	C=0.260
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.855	C=0.145
The Genome Aggregation Database	African	Sub	8730	G=0.974	C=0.026
The Genome Aggregation Database	American	Sub	838	G=0.830	C=0.170
The Genome Aggregation Database	East Asian	Sub	1620	G=0.983	C=0.017
The Genome Aggregation Database	Europe	Sub	18490	G=0.829	C=0.170
The Genome Aggregation Database	Global	Study-wide	29980	G=0.880	C=0.119
The Genome Aggregation Database	Other	Sub	302	G=0.910	C=0.090
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.845	C=0.155

PMID	Title	Author	Journal
26365420	The genetics of alcohol dependence: Twin and SNP-based heritability, and genome-wide association study based on AUDIT scores.	Mbarek H	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs17620991	6E-06	alcohol dependence	26365420

eQTL of rs17620991 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 rs17620991 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.

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	100492303	100495788	E067	-40496
chr7	100492303	100495788	E068	-40496
chr7	100492303	100495788	E069	-40496
chr7	100492303	100495788	E072	-40496
chr7	100491689	100492262	E073	-44022
chr7	100492303	100495788	E073	-40496
chr7	100492303	100495788	E074	-40496
chr7	100492303	100495788	E082	-40496