rs3931840

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

RALB : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0317 (9510/29948,GnomAD)
A==0268 (7827/29116,TOPMED)
A==0369 (1846/5008,1000G)
A==0298 (1147/3854,ALSPAC)
A==0313 (1160/3708,TWINSUK)

Position: chr2:120283771 (GRCh38.p7) (2q14.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 53 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.120283771A>C
GRCh37.p13 chr 2	NC_000002.11:g.121041347A>C

Gene: RALB, v-ral simian leukemia viral oncogene homolog B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RALB transcript	NM_002881.2:c.	N/A	Intron Variant
RALB transcript variant X3	XM_005263724.1:c.	N/A	Intron Variant
RALB transcript variant X4	XM_005263727.1:c.	N/A	Intron Variant
RALB transcript variant X2	XM_005263728.1:c.	N/A	Intron Variant
RALB transcript variant X6	XM_005263729.2:c.	N/A	Intron Variant
RALB transcript variant X1	XM_011511573.1:c.	N/A	Intron Variant
RALB transcript variant X3	XM_011511574.1:c.	N/A	Intron Variant
RALB transcript variant X2	XM_017004621.1:c.	N/A	Intron Variant
RALB transcript variant X7	XM_017004622.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.222	C=0.778
1000Genomes	American	Sub	694	A=0.420	C=0.580
1000Genomes	East Asian	Sub	1008	A=0.597	C=0.403
1000Genomes	Europe	Sub	1006	A=0.292	C=0.708
1000Genomes	Global	Study-wide	5008	A=0.369	C=0.631
1000Genomes	South Asian	Sub	978	A=0.370	C=0.630
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.298	C=0.702
The Genome Aggregation Database	African	Sub	8720	A=0.223	C=0.777
The Genome Aggregation Database	American	Sub	838	A=0.460	C=0.540
The Genome Aggregation Database	East Asian	Sub	1618	A=0.597	C=0.403
The Genome Aggregation Database	Europe	Sub	18470	A=0.333	C=0.666
The Genome Aggregation Database	Global	Study-wide	29948	A=0.317	C=0.682
The Genome Aggregation Database	Other	Sub	302	A=0.160	C=0.840
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.268	C=0.731
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.313	C=0.687

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
rs3931840	0.00064	alcohol dependence	20201924

eQTL of rs3931840 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:121041347	RALB	ENSG00000144118.9	A>C	9.0475e-3	43707	Cortex

meQTL of rs3931840 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg24070213	chr2:121070622		-0.0139917605696485	5.5126e-10

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	121035799	121035891	E067	-5456
chr2	121035975	121036364	E067	-4983
chr2	121012177	121012217	E068	-29130
chr2	121012721	121012825	E068	-28522
chr2	121012883	121013032	E068	-28315
chr2	121013183	121013255	E068	-28092
chr2	121076844	121077011	E068	35497
chr2	121012721	121012825	E069	-28522
chr2	121035799	121035891	E069	-5456
chr2	121035975	121036364	E069	-4983
chr2	121076844	121077011	E069	35497
chr2	121008935	121009057	E070	-32290
chr2	121012177	121012217	E070	-29130
chr2	121015796	121016015	E070	-25332
chr2	121071653	121072125	E070	30306
chr2	121072132	121072182	E070	30785
chr2	121072244	121072478	E070	30897
chr2	121072580	121072640	E070	31233
chr2	121076216	121076300	E070	34869
chr2	121076395	121076597	E070	35048
chr2	121076844	121077011	E070	35497
chr2	121089586	121089756	E070	48239
chr2	121012721	121012825	E071	-28522
chr2	121012883	121013032	E071	-28315
chr2	121013183	121013255	E071	-28092
chr2	121015185	121015387	E071	-25960
chr2	121035975	121036364	E071	-4983
chr2	121076216	121076300	E071	34869
chr2	121076395	121076597	E071	35048
chr2	121076844	121077011	E071	35497
chr2	121012177	121012217	E072	-29130
chr2	121012883	121013032	E072	-28315
chr2	121035975	121036364	E072	-4983
chr2	121012177	121012217	E074	-29130
chr2	121015185	121015387	E074	-25960
chr2	121035799	121035891	E074	-5456
chr2	121035975	121036364	E074	-4983
chr2	121012177	121012217	E081	-29130
chr2	121012721	121012825	E081	-28522
chr2	121071653	121072125	E081	30306
chr2	121072132	121072182	E081	30785
chr2	121072244	121072478	E081	30897
chr2	121076216	121076300	E081	34869
chr2	121076395	121076597	E081	35048
chr2	121076844	121077011	E081	35497
chr2	121012177	121012217	E082	-29130
chr2	121012721	121012825	E082	-28522
chr2	121012883	121013032	E082	-28315
chr2	121013183	121013255	E082	-28092
chr2	121071653	121072125	E082	30306
chr2	121072132	121072182	E082	30785
chr2	121072244	121072478	E082	30897
chr2	121072580	121072640	E082	31233

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	121009569	121011524	E067	-29823
chr2	121009569	121011524	E068	-29823
chr2	121009569	121011524	E069	-29823
chr2	121009569	121011524	E070	-29823
chr2	121009569	121011524	E071	-29823
chr2	121009569	121011524	E072	-29823
chr2	121009569	121011524	E073	-29823
chr2	121009569	121011524	E074	-29823
chr2	121009569	121011524	E081	-29823
chr2	121009569	121011524	E082	-29823