rs6434799

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

DNAH7 : Intron Variant
LOC105373819 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0288 (8633/29970,GnomAD)
C==0294 (8563/29116,TOPMED)
C==0328 (1645/5008,1000G)
C==0262 (1009/3854,ALSPAC)
C==0249 (925/3708,TWINSUK)

Position: chr2:195800359 (GRCh38.p7) (2q32.3)

Phenotype: AD

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 2	NC_000002.12:g.195800359C>T
GRCh37.p13 chr 2	NC_000002.11:g.196665083C>T

Gene: DNAH7, dynein axonemal heavy chain 7(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DNAH7 transcript	NM_018897.2:c.	N/A	Intron Variant
DNAH7 transcript variant X1	XM_011511487.2:c.	N/A	Intron Variant
DNAH7 transcript variant X2	XM_011511488.2:c.	N/A	Intron Variant
DNAH7 transcript variant X2	XM_011511489.2:c.	N/A	Intron Variant
DNAH7 transcript variant X4	XM_011511490.2:c.	N/A	Intron Variant
DNAH7 transcript variant X11	XM_011511497.2:c.	N/A	Intron Variant
DNAH7 transcript variant X5	XM_017004504.1:c.	N/A	Intron Variant
DNAH7 transcript variant X6	XM_011511491.2:c.	N/A	Genic Downstream Transcript Variant
DNAH7 transcript variant X7	XM_011511492.2:c.	N/A	Genic Downstream Transcript Variant
DNAH7 transcript variant X8	XM_011511493.2:c.	N/A	Genic Downstream Transcript Variant
DNAH7 transcript variant X10	XM_011511494.2:c.	N/A	Genic Downstream Transcript Variant
DNAH7 transcript variant X11	XM_011511495.2:c.	N/A	Genic Downstream Transcript Variant
DNAH7 transcript variant X9	XR_922968.2:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC105373819, uncharacterized LOC105373819(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373819 transcript	XR_923736.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.259	T=0.741
1000Genomes	American	Sub	694	C=0.380	T=0.620
1000Genomes	East Asian	Sub	1008	C=0.350	T=0.650
1000Genomes	Europe	Sub	1006	C=0.274	T=0.726
1000Genomes	Global	Study-wide	5008	C=0.328	T=0.672
1000Genomes	South Asian	Sub	978	C=0.420	T=0.580
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.262	T=0.738
The Genome Aggregation Database	African	Sub	8730	C=0.278	T=0.722
The Genome Aggregation Database	American	Sub	834	C=0.360	T=0.640
The Genome Aggregation Database	East Asian	Sub	1612	C=0.367	T=0.633
The Genome Aggregation Database	Europe	Sub	18492	C=0.280	T=0.719
The Genome Aggregation Database	Global	Study-wide	29970	C=0.288	T=0.711
The Genome Aggregation Database	Other	Sub	302	C=0.430	T=0.570
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.294	T=0.705
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.249	T=0.751

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

P-Value

SNP ID	p-value	Traits	Study
rs6434799	0.00048	alcohol dependence	20201924

eQTL of rs6434799 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:196665083	SLC39A10	ENSG00000196950.9	C>T	9.2991e-9	224382	Cerebellum

meQTL of rs6434799 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 )
chr2	196675576	196675812	E070	10493