SNP Detail Info-rs5913935

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0099 (2068/20776,GnomAD)
C==0062 (233/3775,1000G)
C==0141 (524/3708,TWINSUK)
C==0137 (397/2889,ALSPAC)

Position: chrX:56401840 (GRCh38.p7) (Xp11.21)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr X	NC_000023.11:g.56401840C>T
GRCh37.p13 chr X	NC_000023.10:g.56428273C>T

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1003	C=0.011	T=0.989
1000Genomes	American	Sub	524	C=0.090	T=0.910
1000Genomes	East Asian	Sub	764	C=0.000	T=1.000
1000Genomes	Europe	Sub	766	C=0.180	T=0.820
1000Genomes	Global	Study-wide	3775	C=0.062	T=0.938
1000Genomes	South Asian	Sub	718	C=0.050	T=0.950
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	C=0.137	T=0.863
The Genome Aggregation Database	African	Sub	5886	C=0.025	T=0.975
The Genome Aggregation Database	American	Sub	613	C=0.100	T=0.900
The Genome Aggregation Database	East Asian	Sub	1007	C=0.001	T=0.999
The Genome Aggregation Database	Europe	Sub	13087	C=0.137	T=0.862
The Genome Aggregation Database	Global	Study-wide	20776	C=0.099	T=0.900
The Genome Aggregation Database	Other	Sub	183	C=0.360	T=0.640
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.141	T=0.859

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

SNP ID	p-value	Traits	Study
rs5913935	0.000942	alcohol dependence	20201924

eQTL of rs5913935 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	3.9343e-15	-993569	Cerebellum
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	1.7334e-7	-993569	Frontal_Cortex_BA9
ChrX:56428273	RP11-622K12.1	ENSG00000204272.6	C>T	6.8864e-4	-327419	Hypothalamus
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	2.3873e-13	-993569	Hypothalamus
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	1.8542e-15	-993569	Cortex
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	1.1509e-15	-993569	Cerebellar_Hemisphere
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	1.1052e-9	-993569	Anterior_cingulate_cortex
ChrX:56428273	MTHFD1P1	ENSG00000231831.1	C>T	1.5501e-10	-993569	Nucleus_accumbens_basal_ganglia

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

rs5913935