SNP Detail Info-rs4879635

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.32899809G>A
GRCh37.p13 chr 9	NC_000009.11:g.32899807G>A

Gene: APTX, aprataxin(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
APTX transcript variant 6	NM_001195248.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 7	NM_001195249.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 8	NM_001195250.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 9	NM_001195251.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 11	NM_001195252.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 10	NM_001195254.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 2	NM_175069.2:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 1	NM_175073.2:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 12	NR_036576.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 13	NR_036577.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 14	NR_036578.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant 15	NR_036579.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X1	XM_017014831.1:c.	N/A	Intron Variant
APTX transcript variant X2	XM_017014832.1:c.	N/A	Intron Variant
APTX transcript variant X6	XM_017014834.1:c.	N/A	Intron Variant
APTX transcript variant X3	XM_006716791.3:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X14	XM_006716792.2:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X15	XM_011517938.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X16	XM_011517939.2:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X4	XM_017014833.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X7	XM_017014835.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X9	XM_017014836.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X13	XM_017014837.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X24	XM_017014838.1:c.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X5	XR_001746324.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X11	XR_001746325.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X12	XR_001746326.1:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X17	XR_428423.2:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X8	XR_929276.2:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X10	XR_929277.2:n.	N/A	Genic Downstream Transcript Variant
APTX transcript variant X23	XR_929279.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.308	A=0.692
1000Genomes	American	Sub	694	G=0.130	A=0.870
1000Genomes	East Asian	Sub	1008	G=0.091	A=0.909
1000Genomes	Europe	Sub	1006	G=0.146	A=0.854
1000Genomes	Global	Study-wide	5008	G=0.189	A=0.811
1000Genomes	South Asian	Sub	978	G=0.220	A=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.141	A=0.859
The Genome Aggregation Database	African	Sub	8694	G=0.274	A=0.726
The Genome Aggregation Database	American	Sub	838	G=0.110	A=0.890
The Genome Aggregation Database	East Asian	Sub	1620	G=0.088	A=0.912
The Genome Aggregation Database	Europe	Sub	18480	G=0.136	A=0.863
The Genome Aggregation Database	Global	Study-wide	29934	G=0.174	A=0.825
The Genome Aggregation Database	Other	Sub	302	G=0.280	A=0.720
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.205	A=0.794
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.146	A=0.854

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4879635	0.00044	alcohol dependence	20201924

eQTL of rs4879635 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 rs4879635 in Fetal Brain

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

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	32881881	32882003	E067	-17804
chr9	32882137	32882187	E067	-17620
chr9	32881881	32882003	E068	-17804
chr9	32882137	32882187	E068	-17620
chr9	32881881	32882003	E069	-17804
chr9	32882137	32882187	E069	-17620
chr9	32881881	32882003	E071	-17804
chr9	32882137	32882187	E071	-17620
chr9	32881881	32882003	E072	-17804
chr9	32882137	32882187	E072	-17620
chr9	32881881	32882003	E074	-17804
chr9	32882137	32882187	E074	-17620

rs4879635

Genomic Coordinates

Gene: APTX, aprataxin(minus strand)

Population Frequency

P-Value

eQTL of rs4879635 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs4879635 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)