SNP Detail Info-rs2405543

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr X	NC_000023.11:g.32097024G>A
GRCh37.p13 chr X	NC_000023.10:g.32115141G>A
DMD RefSeqGene	LRG_199

Gene: DMD, dystrophin(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DMD transcript variant Dp427c	NM_000109.3:c.	N/A	Intron Variant
DMD transcript variant Dp427m	NM_004006.2:c.	N/A	Intron Variant
DMD transcript variant Dp427p1	NM_004009.3:c.	N/A	Intron Variant
DMD transcript variant Dp427p2	NM_004010.3:c.	N/A	Intron Variant
DMD transcript variant Dp260-1	NM_004011.3:c.	N/A	Intron Variant
DMD transcript variant Dp260-2	NM_004012.3:c.	N/A	Intron Variant
DMD transcript variant Dp140	NM_004013.2:c.	N/A	Intron Variant
DMD transcript variant Dp140c	NM_004020.3:c.	N/A	Intron Variant
DMD transcript variant Dp140b	NM_004021.2:c.	N/A	Intron Variant
DMD transcript variant D140ab	NM_004022.2:c.	N/A	Intron Variant
DMD transcript variant Dp140bc	NM_004023.2:c.	N/A	Intron Variant
DMD transcript variant Dp116	NM_004014.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant Dp71	NM_004015.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant Dp71b	NM_004016.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant Dp71a	NM_004017.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant Dp71ab	NM_004018.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant Dp40	NM_004019.2:c.	N/A	Genic Upstream Transcript Variant
DMD transcript variant X1	XM_006724468.2:c.	N/A	Intron Variant
DMD transcript variant X2	XM_006724469.3:c.	N/A	Intron Variant
DMD transcript variant X3	XM_006724470.3:c.	N/A	Intron Variant
DMD transcript variant X6	XM_006724473.2:c.	N/A	Intron Variant
DMD transcript variant X7	XM_006724474.3:c.	N/A	Intron Variant
DMD transcript variant X8	XM_006724475.2:c.	N/A	Intron Variant
DMD transcript variant X5	XM_011545467.1:c.	N/A	Intron Variant
DMD transcript variant X9	XM_011545468.2:c.	N/A	Intron Variant
DMD transcript variant X4	XM_017029328.1:c.	N/A	Intron Variant
DMD transcript variant X13	XM_017029331.1:c.	N/A	Intron Variant
DMD transcript variant X12	XM_011545469.1:c.	N/A	Genic Downstream Transcript Variant
DMD transcript variant X10	XM_017029329.1:c.	N/A	Genic Downstream Transcript Variant
DMD transcript variant X11	XM_017029330.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1003	G=0.878	A=0.122
1000Genomes	American	Sub	524	G=0.940	A=0.060
1000Genomes	East Asian	Sub	764	G=0.810	A=0.190
1000Genomes	Europe	Sub	766	G=0.990	A=0.010
1000Genomes	Global	Study-wide	3775	G=0.909	A=0.091
1000Genomes	South Asian	Sub	718	G=0.950	A=0.050
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	G=0.993	A=0.007
The Genome Aggregation Database	African	Sub	5890	G=0.869	A=0.131
The Genome Aggregation Database	American	Sub	609	G=0.940	A=0.060
The Genome Aggregation Database	East Asian	Sub	974	G=0.830	A=0.170
The Genome Aggregation Database	Europe	Sub	13179	G=0.983	A=0.016
The Genome Aggregation Database	Global	Study-wide	20842	G=0.942	A=0.057
The Genome Aggregation Database	Other	Sub	190	G=0.960	A=0.040
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.991	A=0.009

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
rs2405543	0.00084	alcohol dependence	20201924

eQTL of rs2405543 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 rs2405543 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 )
chrX	32071433	32071483	E067	-43658
chrX	32071676	32071743	E067	-43398

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chrX	32128955	32129031	E068	13814
chrX	32092734	32092820	E072	-22321
chrX	32092964	32093036	E072	-22105
chrX	32093113	32093183	E072	-21958

rs2405543

Genomic Coordinates

Gene: DMD, dystrophin(minus strand)

Population Frequency

P-Value

eQTL of rs2405543 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2405543 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)