rs2039617

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CC2D2B : Intron Variant
ENTPD1-AS1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0230 (6723/29118,TOPMED)
A=0227 (6587/28994,GnomAD)
A=0362 (1811/5008,1000G)
A=0075 (288/3854,ALSPAC)
A=0072 (267/3708,TWINSUK)

Position: chr10:95999446 (GRCh38.p7) (10q24.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 19 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 10	NC_000010.11:g.95999446G>A
GRCh37.p13 chr 10	NC_000010.10:g.97759203G>A

Gene: CC2D2B, coiled-coil and C2 domain containing 2B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CC2D2B transcript variant 2	NM_001001732.3:c.	N/A	Genic Upstream Transcript Variant
CC2D2B transcript variant 1	NM_001159747.1:c.	N/A	Genic Upstream Transcript Variant
CC2D2B transcript variant X1	XM_011539789.2:c.	N/A	Intron Variant
CC2D2B transcript variant X2	XM_011539790.2:c.	N/A	Intron Variant
CC2D2B transcript variant X3	XM_011539791.2:c.	N/A	Intron Variant
CC2D2B transcript variant X6	XM_011539793.2:c.	N/A	5 Prime UTR Variant
CC2D2B transcript variant X7	XM_011539795.2:c.	N/A	5 Prime UTR Variant
CC2D2B transcript variant X5	XM_011539792.2:c.	N/A	Genic Upstream Transcript Variant
CC2D2B transcript variant X4	XM_017016240.1:c.	N/A	Genic Upstream Transcript Variant

Gene: ENTPD1-AS1, ENTPD1 antisense RNA 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ENTPD1-AS1 transcript variant 1	NR_038444.1:n.	N/A	Intron Variant
ENTPD1-AS1 transcript variant 2	NR_134320.1:n.	N/A	Genic Downstream Transcript Variant
ENTPD1-AS1 transcript variant 3	NR_134321.1:n.	N/A	Genic Downstream Transcript Variant
ENTPD1-AS1 transcript variant 4	NR_134322.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.612	A=0.388
1000Genomes	American	Sub	694	G=0.860	A=0.140
1000Genomes	East Asian	Sub	1008	G=0.219	A=0.781
1000Genomes	Europe	Sub	1006	G=0.893	A=0.107
1000Genomes	Global	Study-wide	5008	G=0.638	A=0.362
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.925	A=0.075
The Genome Aggregation Database	African	Sub	8554	G=0.633	A=0.367
The Genome Aggregation Database	American	Sub	798	G=0.830	A=0.170
The Genome Aggregation Database	East Asian	Sub	1614	G=0.187	A=0.813
The Genome Aggregation Database	Europe	Sub	17728	G=0.890	A=0.109
The Genome Aggregation Database	Global	Study-wide	28994	G=0.772	A=0.227
The Genome Aggregation Database	Other	Sub	300	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.769	A=0.230
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.928	A=0.072

PMID	Title	Author	Journal
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs2039617	1.4E-05	alcohol dependence	21956439

eQTL of rs2039617 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 rs2039617 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 )
chr10	97713661	97713762	E070	-45441
chr10	97713814	97713871	E070	-45332
chr10	97805899	97806082	E070	46696
chr10	97806108	97806158	E070	46905
chr10	97806257	97806320	E070	47054
chr10	97806484	97806534	E070	47281
chr10	97806550	97806604	E070	47347
chr10	97802237	97802304	E071	43034
chr10	97776846	97777389	E072	17643
chr10	97805899	97806082	E081	46696
chr10	97806108	97806158	E081	46905
chr10	97806257	97806320	E081	47054
chr10	97802195	97802235	E082	42992
chr10	97806257	97806320	E082	47054
chr10	97806484	97806534	E082	47281
chr10	97806550	97806604	E082	47347
chr10	97806772	97806832	E082	47569
chr10	97806916	97807044	E082	47713
chr10	97807176	97807226	E082	47973

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	97802479	97804968	E067	43276
chr10	97802479	97804968	E068	43276
chr10	97802479	97804968	E069	43276
chr10	97802479	97804968	E070	43276
chr10	97802479	97804968	E071	43276
chr10	97802479	97804968	E072	43276
chr10	97802479	97804968	E073	43276
chr10	97802479	97804968	E074	43276
chr10	97802479	97804968	E081	43276
chr10	97802479	97804968	E082	43276