rs6743998

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

DNAH7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0325 (9684/29748,GnomAD)
T==0334 (9738/29118,TOPMED)
T==0431 (2158/5008,1000G)
T==0257 (992/3854,ALSPAC)
T==0245 (907/3708,TWINSUK)

Position: chr2:195811765 (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.195811765T>C
GRCh37.p13 chr 2	NC_000002.11:g.196676489T>C

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.345	C=0.655
1000Genomes	American	Sub	694	T=0.480	C=0.520
1000Genomes	East Asian	Sub	1008	T=0.634	C=0.366
1000Genomes	Europe	Sub	1006	T=0.279	C=0.721
1000Genomes	Global	Study-wide	5008	T=0.431	C=0.569
1000Genomes	South Asian	Sub	978	T=0.460	C=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.257	C=0.743
The Genome Aggregation Database	African	Sub	8664	T=0.332	C=0.668
The Genome Aggregation Database	American	Sub	834	T=0.490	C=0.510
The Genome Aggregation Database	East Asian	Sub	1608	T=0.664	C=0.336
The Genome Aggregation Database	Europe	Sub	18340	T=0.283	C=0.716
The Genome Aggregation Database	Global	Study-wide	29748	T=0.325	C=0.674
The Genome Aggregation Database	Other	Sub	302	T=0.410	C=0.590
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.334	C=0.665
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.245	C=0.755

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

P-Value

SNP ID	p-value	Traits	Study
rs6743998	0.000757	alcohol dependence	21314694

eQTL of rs6743998 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:196676489	SLC39A10	ENSG00000196950.9	T>C	9.2991e-9	235788	Cerebellum

meQTL of rs6743998 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	-677