rs10429416

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

LOC100507516 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0143 (4273/29886,GnomAD)
A=0170 (4963/29118,TOPMED)
A=0155 (775/5008,1000G)
A=0104 (401/3854,ALSPAC)
A=0108 (399/3708,TWINSUK)

Position: chr8:53453931 (GRCh38.p7) (8q11.23)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.53453931C>A
GRCh37.p13 chr 8	NC_000008.10:g.54366491C>A

Gene: LOC100507516, uncharacterized LOC100507516(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507516 transcript variant X2	XR_001745900.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X3	XR_001745901.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X4	XR_001745902.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X5	XR_001745903.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X6	XR_001745904.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X7	XR_001745905.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X8	XR_001745906.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X9	XR_001745907.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X10	XR_001745908.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X11	XR_001745909.1:n.	N/A	Intron Variant
LOC100507516 transcript variant X12	XR_001745910.1:n.	N/A	Genic Downstream Transcript Variant
LOC100507516 transcript variant X13	XR_001745911.1:n.	N/A	Genic Downstream Transcript Variant
LOC100507516 transcript variant X14	XR_001745912.1:n.	N/A	Genic Downstream Transcript Variant
LOC100507516 transcript variant X1	XR_928879.2:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.699	A=0.301
1000Genomes	American	Sub	694	C=0.910	A=0.090
1000Genomes	East Asian	Sub	1008	C=0.904	A=0.096
1000Genomes	Europe	Sub	1006	C=0.903	A=0.097
1000Genomes	Global	Study-wide	5008	C=0.845	A=0.155
1000Genomes	South Asian	Sub	978	C=0.880	A=0.120
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.896	A=0.104
The Genome Aggregation Database	African	Sub	8708	C=0.722	A=0.278
The Genome Aggregation Database	American	Sub	838	C=0.920	A=0.080
The Genome Aggregation Database	East Asian	Sub	1588	C=0.918	A=0.082
The Genome Aggregation Database	Europe	Sub	18450	C=0.913	A=0.086
The Genome Aggregation Database	Global	Study-wide	29886	C=0.857	A=0.143
The Genome Aggregation Database	Other	Sub	302	C=0.780	A=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.829	A=0.170
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.892	A=0.108

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs10429416	3.17E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs10429416 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 rs10429416 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr8	54408075	54408131	E070	41584