SNP Detail Info-rs11164938

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

FNBP1L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0478 (14315/29934,GnomAD)
G=0386 (11254/29118,TOPMED)
G=0447 (2241/5008,1000G)
A==0386 (1489/3854,ALSPAC)
A==0387 (1436/3708,TWINSUK)

Position: chr1:93474313 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 26 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.93474313A>G
GRCh37.p13 chr 1	NC_000001.10:g.93939870A>G

Molecule type	Change	Amino acid[Codon]	SO Term
FNBP1L transcript variant 1	NM_001024948.2:c.	N/A	Intron Variant
FNBP1L transcript variant 3	NM_001164473.2:c.	N/A	Intron Variant
FNBP1L transcript variant 2	NM_017737.4:c.	N/A	Intron Variant
FNBP1L transcript variant X1	XM_011541625.2:c.	N/A	Intron Variant
FNBP1L transcript variant X2	XM_017001533.1:c.	N/A	Intron Variant
FNBP1L transcript variant X3	XR_001737248.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.933	G=0.067
1000Genomes	American	Sub	694	A=0.470	G=0.530
1000Genomes	East Asian	Sub	1008	A=0.392	G=0.608
1000Genomes	Europe	Sub	1006	A=0.394	G=0.606
1000Genomes	Global	Study-wide	5008	A=0.553	G=0.447
1000Genomes	South Asian	Sub	978	A=0.430	G=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.386	G=0.614
The Genome Aggregation Database	African	Sub	8728	A=0.850	G=0.150
The Genome Aggregation Database	American	Sub	836	A=0.510	G=0.490
The Genome Aggregation Database	East Asian	Sub	1612	A=0.393	G=0.607
The Genome Aggregation Database	Europe	Sub	18456	A=0.380	G=0.619
The Genome Aggregation Database	Global	Study-wide	29934	A=0.521	G=0.478
The Genome Aggregation Database	Other	Sub	302	A=0.380	G=0.620
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.613	G=0.386
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.387	G=0.613

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs11164938	0.000549	alcohol dependence	21314694

eQTL of rs11164938 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93939870	RP4-717I23.3	ENSG00000223745.3	A>G	0.0000e+0	128426	Cerebellum
Chr1:93939870	RP4-717I23.3	ENSG00000223745.3	A>G	2.3189e-23	128426	Frontal_Cortex_BA9
Chr1:93939870	RP4-717I23.3	ENSG00000223745.3	A>G	0.0000e+0	128426	Cortex
Chr1:93939870	TMED5	ENSG00000117500.8	A>G	1.4315e-3	311103	Cerebellar_Hemisphere
Chr1:93939870	RP4-717I23.3	ENSG00000223745.3	A>G	1.8720e-25	128426	Cerebellar_Hemisphere
Chr1:93939870	RP4-717I23.3	ENSG00000223745.3	A>G	0.0000e+0	128426	Nucleus_accumbens_basal_ganglia

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	93936788	93937154	E070	-2716
chr1	93920909	93921069	E082	-18801
chr1	93925225	93925295	E082	-14575

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93912414	93913035	E067	-26835
chr1	93913083	93915249	E067	-24621
chr1	93912414	93913035	E068	-26835
chr1	93913083	93915249	E068	-24621
chr1	93916437	93916477	E068	-23393
chr1	93912414	93913035	E069	-26835
chr1	93912414	93913035	E070	-26835
chr1	93913083	93915249	E070	-24621
chr1	93916033	93916146	E070	-23724
chr1	93916196	93916248	E070	-23622
chr1	93916437	93916477	E070	-23393
chr1	93912414	93913035	E071	-26835
chr1	93913083	93915249	E071	-24621
chr1	93912414	93913035	E072	-26835
chr1	93913083	93915249	E072	-24621
chr1	93912414	93913035	E073	-26835
chr1	93913083	93915249	E073	-24621
chr1	93912414	93913035	E074	-26835
chr1	93913083	93915249	E074	-24621
chr1	93912414	93913035	E081	-26835
chr1	93913083	93915249	E081	-24621
chr1	93912414	93913035	E082	-26835
chr1	93913083	93915249	E082	-24621
chr1	93916033	93916146	E082	-23724
chr1	93916196	93916248	E082	-23622
chr1	93916437	93916477	E082	-23393

rs11164938