rs16992410

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

HDGFRP2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0096 (2887/29842,GnomAD)
G=0084 (2459/29118,TOPMED)
G=0114 (573/5008,1000G)
G=0124 (479/3854,ALSPAC)
G=0123 (457/3708,TWINSUK)

Position: chr19:4487809 (GRCh38.p7) (19p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 106 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.4487809A>G
GRCh37.p13 chr 19	NC_000019.9:g.4487806A>G

Gene: HDGFRP2, hepatoma-derived growth factor-related protein 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HDGFL2 transcript variant 1	NM_001001520.2:c.	N/A	Intron Variant
HDGFL2 transcript variant 2	NM_032631.3:c.	N/A	Intron Variant
HDGFRP2 transcript variant X1	XM_011528375.2:c.	N/A	Intron Variant
HDGFRP2 transcript variant X3	XM_011528376.2:c.	N/A	Intron Variant
HDGFRP2 transcript variant X2	XM_011528377.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.976	G=0.024
1000Genomes	American	Sub	694	A=0.900	G=0.100
1000Genomes	East Asian	Sub	1008	A=0.916	G=0.084
1000Genomes	Europe	Sub	1006	A=0.847	G=0.153
1000Genomes	Global	Study-wide	5008	A=0.886	G=0.114
1000Genomes	South Asian	Sub	978	A=0.760	G=0.240
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.876	G=0.124
The Genome Aggregation Database	African	Sub	8710	A=0.961	G=0.039
The Genome Aggregation Database	American	Sub	838	A=0.910	G=0.090
The Genome Aggregation Database	East Asian	Sub	1616	A=0.918	G=0.082
The Genome Aggregation Database	Europe	Sub	18376	A=0.874	G=0.125
The Genome Aggregation Database	Global	Study-wide	29842	A=0.903	G=0.096
The Genome Aggregation Database	Other	Sub	302	A=0.860	G=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.915	G=0.084
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.877	G=0.123

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
rs16992410	0.000606	alcohol dependence	20201924

eQTL of rs16992410 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 rs16992410 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 )
chr19	4448998	4449970	E067	-37836
chr19	4475249	4475299	E067	-12507
chr19	4475416	4475484	E067	-12322
chr19	4475560	4475667	E067	-12139
chr19	4492050	4492320	E067	4244
chr19	4504980	4505216	E067	17174
chr19	4505232	4505382	E067	17426
chr19	4517354	4517413	E067	29548
chr19	4517460	4517771	E067	29654
chr19	4448544	4448946	E068	-38860
chr19	4448998	4449970	E068	-37836
chr19	4475249	4475299	E068	-12507
chr19	4475416	4475484	E068	-12322
chr19	4475560	4475667	E068	-12139
chr19	4495676	4495805	E068	7870
chr19	4495831	4495890	E068	8025
chr19	4495922	4495976	E068	8116
chr19	4496156	4496234	E068	8350
chr19	4517354	4517413	E068	29548
chr19	4519228	4519327	E068	31422
chr19	4519400	4519495	E068	31594
chr19	4519604	4520307	E068	31798
chr19	4448998	4449970	E069	-37836
chr19	4475249	4475299	E069	-12507
chr19	4475416	4475484	E069	-12322
chr19	4475560	4475667	E069	-12139
chr19	4517354	4517413	E069	29548
chr19	4517460	4517771	E069	29654
chr19	4518230	4519150	E069	30424
chr19	4519228	4519327	E069	31422
chr19	4535880	4535983	E069	48074
chr19	4475416	4475484	E070	-12322
chr19	4535880	4535983	E070	48074
chr19	4448544	4448946	E071	-38860
chr19	4448998	4449970	E071	-37836
chr19	4450351	4450401	E071	-37405
chr19	4504305	4504838	E071	16499
chr19	4504856	4504919	E071	17050
chr19	4504980	4505216	E071	17174
chr19	4505232	4505382	E071	17426
chr19	4505391	4505467	E071	17585
chr19	4505490	4505598	E071	17684
chr19	4505644	4505777	E071	17838
chr19	4519228	4519327	E071	31422
chr19	4519400	4519495	E071	31594
chr19	4519604	4520307	E071	31798
chr19	4535880	4535983	E071	48074
chr19	4448544	4448946	E072	-38860
chr19	4448998	4449970	E072	-37836
chr19	4475249	4475299	E072	-12507
chr19	4492050	4492320	E072	4244
chr19	4492516	4492587	E072	4710
chr19	4492646	4492736	E072	4840
chr19	4492758	4492808	E072	4952
chr19	4492849	4493040	E072	5043
chr19	4493099	4493201	E072	5293
chr19	4517354	4517413	E072	29548
chr19	4517460	4517771	E072	29654
chr19	4519228	4519327	E072	31422
chr19	4519400	4519495	E072	31594
chr19	4439892	4439942	E073	-47864
chr19	4439966	4440048	E073	-47758
chr19	4448291	4448530	E073	-39276
chr19	4448544	4448946	E073	-38860
chr19	4448998	4449970	E073	-37836
chr19	4450351	4450401	E073	-37405
chr19	4450598	4450707	E073	-37099
chr19	4454482	4454598	E073	-33208
chr19	4475249	4475299	E073	-12507
chr19	4475416	4475484	E073	-12322
chr19	4475560	4475667	E073	-12139
chr19	4492050	4492320	E073	4244
chr19	4503928	4503972	E073	16122
chr19	4504305	4504838	E073	16499
chr19	4504856	4504919	E073	17050
chr19	4504980	4505216	E073	17174
chr19	4505232	4505382	E073	17426
chr19	4505391	4505467	E073	17585
chr19	4505490	4505598	E073	17684
chr19	4448998	4449970	E074	-37836
chr19	4517354	4517413	E074	29548
chr19	4517460	4517771	E074	29654
chr19	4438280	4438330	E081	-49476
chr19	4438511	4438561	E081	-49245
chr19	4439360	4439709	E081	-48097
chr19	4439892	4439942	E081	-47864
chr19	4439966	4440048	E081	-47758
chr19	4440135	4440236	E081	-47570
chr19	4440250	4440300	E081	-47506
chr19	4440616	4440751	E081	-47055
chr19	4440770	4440836	E081	-46970
chr19	4442458	4442860	E081	-44946
chr19	4442886	4442984	E081	-44822
chr19	4448291	4448530	E081	-39276
chr19	4448544	4448946	E081	-38860
chr19	4448998	4449970	E081	-37836
chr19	4475249	4475299	E081	-12507
chr19	4475416	4475484	E081	-12322
chr19	4475560	4475667	E081	-12139
chr19	4535880	4535983	E081	48074
chr19	4439360	4439709	E082	-48097
chr19	4439892	4439942	E082	-47864
chr19	4439966	4440048	E082	-47758
chr19	4440135	4440236	E082	-47570
chr19	4448544	4448946	E082	-38860
chr19	4448998	4449970	E082	-37836

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	4454649	4458597	E067	-29209
chr19	4470982	4473642	E067	-14164
chr19	4454649	4458597	E068	-29209
chr19	4470982	4473642	E068	-14164
chr19	4454649	4458597	E069	-29209
chr19	4470982	4473642	E069	-14164
chr19	4454649	4458597	E070	-29209
chr19	4470982	4473642	E070	-14164
chr19	4454649	4458597	E071	-29209
chr19	4470982	4473642	E071	-14164
chr19	4454649	4458597	E072	-29209
chr19	4470982	4473642	E072	-14164
chr19	4454649	4458597	E073	-29209
chr19	4470982	4473642	E073	-14164
chr19	4470982	4473642	E074	-14164
chr19	4454649	4458597	E082	-29209
chr19	4470982	4473642	E082	-14164