rs4847431

Organism: Homo sapiens

Alleles: G>A / G>C

Gene : Feature

FNBP1L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0490 (14635/29864,GnomAD)
C=0434 (12658/29118,TOPMED)
C=0487 (2437/5008,1000G)
G==0386 (1488/3854,ALSPAC)
G==0385 (1427/3708,TWINSUK)

Position: chr1:93519247 (GRCh38.p7) (1p22.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.93519247G>A
GRCh38.p7 chr 1	NC_000001.11:g.93519247G>C
GRCh37.p13 chr 1	NC_000001.10:g.93984804G>A
GRCh37.p13 chr 1	NC_000001.10:g.93984804G>C

Gene: FNBP1L, formin binding protein 1 like(plus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.811	C=0.189
1000Genomes	American	Sub	694	G=0.460	C=0.540
1000Genomes	East Asian	Sub	1008	G=0.366	C=0.634
1000Genomes	Europe	Sub	1006	G=0.393	C=0.607
1000Genomes	Global	Study-wide	5008	G=0.513	C=0.487
1000Genomes	South Asian	Sub	978	G=0.430	C=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.386	C=0.614
The Genome Aggregation Database	African	Sub	8688	G=0.747	C=0.253
The Genome Aggregation Database	American	Sub	832	G=0.500	C=0.50,
The Genome Aggregation Database	East Asian	Sub	1612	G=0.377	C=0.623
The Genome Aggregation Database	Europe	Sub	18434	G=0.380	C=0.619
The Genome Aggregation Database	Global	Study-wide	29864	G=0.490	C=0.509
The Genome Aggregation Database	Other	Sub	298	G=0.390	C=0.61,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.565	C=0.434
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.385	C=0.615

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet
14740319	Matching strategies for genetic association studies in structured populations.	Hinds DA	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4847431	3.92E-05	nicotine dependence	17158188

eQTL of rs4847431 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93984804	RP4-717I23.3	ENSG00000223745.3	G>C	0.0000e+0	173360	Cerebellum
Chr1:93984804	RP4-717I23.3	ENSG00000223745.3	G>C	2.3189e-23	173360	Frontal_Cortex_BA9
Chr1:93984804	RP4-717I23.3	ENSG00000223745.3	G>C	0.0000e+0	173360	Cortex
Chr1:93984804	TMED5	ENSG00000117500.8	G>C	1.4315e-3	356037	Cerebellar_Hemisphere
Chr1:93984804	RP4-717I23.3	ENSG00000223745.3	G>C	1.8720e-25	173360	Cerebellar_Hemisphere
Chr1:93984804	RP4-717I23.3	ENSG00000223745.3	G>C	0.0000e+0	173360	Nucleus_accumbens_basal_ganglia

meQTL of rs4847431 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.