rs4700575

Organism: Homo sapiens

Alleles: T>A / T>G

Gene : Feature

LOC107986417 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0234 (7008/29832,GnomAD)
G=0284 (8272/29118,TOPMED)
G=0229 (1149/5008,1000G)
G=0217 (837/3854,ALSPAC)
G=0205 (761/3708,TWINSUK)

Position: chr5:63300149 (GRCh38.p7) (5q12.1)

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 5	NC_000005.10:g.63300149T>A
GRCh38.p7 chr 5	NC_000005.10:g.63300149T>G
GRCh37.p13 chr 5	NC_000005.9:g.62595976T>A
GRCh37.p13 chr 5	NC_000005.9:g.62595976T>G

Gene: LOC107986417, uncharacterized LOC107986417(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107986417 transcript variant X1	XR_001742676.1:n....XR_001742676.1:n.6301T>A	T>A	Non Coding Transcript Variant
LOC107986417 transcript variant X1	XR_001742676.1:n....XR_001742676.1:n.6301T>G	T>G	Non Coding Transcript Variant
LOC107986417 transcript variant X2	XR_001742677.1:n....XR_001742677.1:n.6301T>A	T>A	Non Coding Transcript Variant
LOC107986417 transcript variant X2	XR_001742677.1:n....XR_001742677.1:n.6301T>G	T>G	Non Coding Transcript Variant
LOC107986417 transcript variant X3	XR_001742678.1:n....XR_001742678.1:n.6301T>A	T>A	Non Coding Transcript Variant
LOC107986417 transcript variant X3	XR_001742678.1:n....XR_001742678.1:n.6301T>G	T>G	Non Coding Transcript Variant
LOC107986417 transcript variant X4	XR_001742679.1:n....XR_001742679.1:n.6301T>A	T>A	Non Coding Transcript Variant
LOC107986417 transcript variant X4	XR_001742679.1:n....XR_001742679.1:n.6301T>G	T>G	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.553	G=0.447
1000Genomes	American	Sub	694	T=0.780	G=0.220
1000Genomes	East Asian	Sub	1008	T=0.882	G=0.118
1000Genomes	Europe	Sub	1006	T=0.806	G=0.194
1000Genomes	Global	Study-wide	5008	T=0.771	G=0.229
1000Genomes	South Asian	Sub	978	T=0.910	G=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.783	G=0.217
The Genome Aggregation Database	African	Sub	8688	T=0.614	A=0.000
The Genome Aggregation Database	American	Sub	828	T=0.810	A=0.00,
The Genome Aggregation Database	East Asian	Sub	1594	T=0.859	A=0.000
The Genome Aggregation Database	Europe	Sub	18420	T=0.826	A=0.000
The Genome Aggregation Database	Global	Study-wide	29832	T=0.765	A=0.000
The Genome Aggregation Database	Other	Sub	302	T=0.750	A=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.715	G=0.284
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.795	G=0.205

PMID	Title	Author	Journal
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology
22488850	Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs4700575	2.8E-07	alcohol and nictotine co-dependence	22488850

eQTL of rs4700575 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 rs4700575 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.