rs12898370

Organism: Homo sapiens

Alleles: A>C / A>T

Gene : Feature

HMG20A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0249 (7450/29898,GnomAD)
T=0217 (6336/29118,TOPMED)
T=0176 (881/5008,1000G)
T=0321 (1238/3854,ALSPAC)
T=0326 (1210/3708,TWINSUK)

Position: chr15:77516256 (GRCh38.p7) (15q24.3)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 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 15	NC_000015.10:g.77516256A>C
GRCh38.p7 chr 15	NC_000015.10:g.77516256A>T
GRCh37.p13 chr 15	NC_000015.9:g.77808598A>C
GRCh37.p13 chr 15	NC_000015.9:g.77808598A>T

Gene: HMG20A, high mobility group 20A(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HMG20A transcript variant 2	NM_001304504.1:c.	N/A	Genic Downstream Transcript Variant
HMG20A transcript variant 3	NM_001304505.1:c.	N/A	Genic Downstream Transcript Variant
HMG20A transcript variant 1	NM_018200.3:c.	N/A	Genic Downstream Transcript Variant
HMG20A transcript variant X1	XM_011521158.2:c.	N/A	Intron Variant
HMG20A transcript variant X2	XR_001751049.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.919	T=0.081
1000Genomes	American	Sub	694	A=0.720	T=0.280
1000Genomes	East Asian	Sub	1008	A=0.885	T=0.115
1000Genomes	Europe	Sub	1006	A=0.700	T=0.300
1000Genomes	Global	Study-wide	5008	A=0.824	T=0.176
1000Genomes	South Asian	Sub	978	A=0.830	T=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.679	T=0.321
The Genome Aggregation Database	African	Sub	8710	A=0.890	T=0.110
The Genome Aggregation Database	American	Sub	838	A=0.760	T=0.24,
The Genome Aggregation Database	East Asian	Sub	1620	A=0.884	T=0.115
The Genome Aggregation Database	Europe	Sub	18428	A=0.673	T=0.326
The Genome Aggregation Database	Global	Study-wide	29898	A=0.750	T=0.249
The Genome Aggregation Database	Other	Sub	302	A=0.700	T=0.30,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.782	T=0.217
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.674	T=0.326

PMID	Title	Author	Journal
28990359	Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors.	Polimanti R	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs12898370	4E-08	alcohol dependence	28990359

eQTL of rs12898370 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:77808598	PEAK1	ENSG00000173517.6	A>T	4.1028e-7	96112	Cerebellum
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	5.7232e-6	-9284	Cerebellum
Chr15:77808598	RP11-307C19.3	ENSG00000259666.1	A>T	3.9399e-12	-125508	Cerebellum
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	6.4875e-5	-9284	Frontal_Cortex_BA9
Chr15:77808598	PEAK1	ENSG00000173517.6	A>T	2.1912e-5	96112	Cortex
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	9.9289e-7	-9284	Cortex
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	1.5346e-4	-9284	Cerebellar_Hemisphere
Chr15:77808598	RP11-307C19.3	ENSG00000259666.1	A>T	1.4265e-5	-125508	Cerebellar_Hemisphere
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	9.2520e-4	-9284	Caudate_basal_ganglia
Chr15:77808598	RP11-307C19.1	ENSG00000259362.2	A>T	1.6618e-4	-9284	Brain_Spinal_cord_cervical
Chr15:77808598	LINGO1	ENSG00000169783.8	A>T	7.4035e-5	-304644	Putamen_basal_ganglia

meQTL of rs12898370 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.