rs9297647

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC105375732 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0428 (12814/29902,GnomAD)
G=0467 (13616/29118,TOPMED)
G=0345 (1727/5008,1000G)
G=0399 (1536/3854,ALSPAC)
G=0406 (1504/3708,TWINSUK)

Position: chr8:121671200 (GRCh38.p7) (8q24.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 43 Enhancers around

Promoter: 12 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.121671200A>G
GRCh37.p13 chr 8	NC_000008.10:g.122683440A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105375732 transcript variant X1	XR_928597.2:n.	N/A	Intron Variant
LOC105375732 transcript variant X2	XR_928598.2:n.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.415	G=0.585
1000Genomes	American	Sub	694	A=0.640	G=0.360
1000Genomes	East Asian	Sub	1008	A=0.859	G=0.141
1000Genomes	Europe	Sub	1006	A=0.633	G=0.367
1000Genomes	Global	Study-wide	5008	A=0.655	G=0.345
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.601	G=0.399
The Genome Aggregation Database	African	Sub	8702	A=0.452	G=0.548
The Genome Aggregation Database	American	Sub	834	A=0.620	G=0.380
The Genome Aggregation Database	East Asian	Sub	1620	A=0.860	G=0.140
The Genome Aggregation Database	Europe	Sub	18444	A=0.600	G=0.399
The Genome Aggregation Database	Global	Study-wide	29902	A=0.571	G=0.428
The Genome Aggregation Database	Other	Sub	302	A=0.580	G=0.420
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.532	G=0.467
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.594	G=0.406

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

SNP ID	p-value	Traits	Study
rs9297647	0.000938	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
cg21781600	chr8:122651575	HAS2AS\|HAS2	0.0169642282633017	8.3654e-10

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr8	122638154	122639727	E068	-43713
chr8	122681364	122681444	E068	-1996
chr8	122640008	122640255	E069	-43185
chr8	122640265	122640379	E069	-43061
chr8	122640401	122640467	E069	-42973
chr8	122640476	122640560	E069	-42880
chr8	122640653	122640777	E069	-42663
chr8	122640815	122640925	E069	-42515
chr8	122640950	122641165	E069	-42275
chr8	122638154	122639727	E071	-43713
chr8	122639753	122639803	E071	-43637
chr8	122640008	122640255	E071	-43185
chr8	122640265	122640379	E071	-43061
chr8	122640401	122640467	E071	-42973
chr8	122640476	122640560	E071	-42880
chr8	122640653	122640777	E071	-42663
chr8	122640815	122640925	E071	-42515
chr8	122640950	122641165	E071	-42275
chr8	122681364	122681444	E071	-1996
chr8	122681468	122682247	E071	-1193
chr8	122640008	122640255	E072	-43185
chr8	122640265	122640379	E072	-43061
chr8	122640401	122640467	E072	-42973
chr8	122640476	122640560	E072	-42880
chr8	122640653	122640777	E072	-42663
chr8	122640815	122640925	E072	-42515
chr8	122640950	122641165	E072	-42275
chr8	122643743	122644542	E072	-38898
chr8	122681468	122682247	E072	-1193
chr8	122638154	122639727	E074	-43713
chr8	122639753	122639803	E074	-43637
chr8	122640008	122640255	E074	-43185
chr8	122640265	122640379	E074	-43061
chr8	122640401	122640467	E074	-42973
chr8	122640476	122640560	E074	-42880
chr8	122640653	122640777	E074	-42663
chr8	122640815	122640925	E074	-42515
chr8	122640950	122641165	E074	-42275
chr8	122641386	122641483	E074	-41957
chr8	122643029	122643144	E074	-40296
chr8	122643170	122643292	E074	-40148
chr8	122643363	122643521	E074	-39919
chr8	122643576	122643626	E074	-39814

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	122650933	122653369	E067	-30071
chr8	122653454	122655319	E067	-28121
chr8	122650933	122653369	E068	-30071
chr8	122653454	122655319	E068	-28121
chr8	122650933	122653369	E069	-30071
chr8	122653454	122655319	E069	-28121
chr8	122650933	122653369	E071	-30071
chr8	122653454	122655319	E071	-28121
chr8	122650933	122653369	E072	-30071
chr8	122653454	122655319	E072	-28121
chr8	122650933	122653369	E074	-30071
chr8	122653454	122655319	E074	-28121