rs4810479

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0321 (9622/29918,GnomAD)
C==0340 (9900/29118,TOPMED)
C==0454 (2274/5008,1000G)
C==0249 (961/3854,ALSPAC)
C==0242 (899/3708,TWINSUK)

Position: chr20:45916409 (GRCh38.p7) (20q13.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 10 publication(s)

Genomic View: See rs on genome

Enhancer: 109 Enhancers around

Promoter: 37 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.45916409C>T
GRCh37.p13 chr 20	NC_000020.10:g.44545048C>T
PLTP RefSeqGene	NG_012115.1:g.739G>A

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.398	T=0.602
1000Genomes	American	Sub	694	C=0.470	T=0.530
1000Genomes	East Asian	Sub	1008	C=0.629	T=0.371
1000Genomes	Europe	Sub	1006	C=0.288	T=0.712
1000Genomes	Global	Study-wide	5008	C=0.454	T=0.546
1000Genomes	South Asian	Sub	978	C=0.510	T=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.249	T=0.751
The Genome Aggregation Database	African	Sub	8710	C=0.394	T=0.606
The Genome Aggregation Database	American	Sub	836	C=0.530	T=0.470
The Genome Aggregation Database	East Asian	Sub	1612	C=0.614	T=0.386
The Genome Aggregation Database	Europe	Sub	18458	C=0.253	T=0.746
The Genome Aggregation Database	Global	Study-wide	29918	C=0.321	T=0.678
The Genome Aggregation Database	Other	Sub	302	C=0.270	T=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.340	T=0.660
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.242	T=0.758

PMID	Title	Author	Journal
19936222	Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.	Chasman DI	PLoS Genet
21283740	Large-scale candidate gene analysis of HDL particle features.	Kaess BM	PLoS One
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
21597005	An increased burden of common and rare lipid-associated risk alleles contributes to the phenotypic spectrum of hypertriglyceridemia.	Johansen CT	Arterioscler Thromb Vasc Biol
26009633	PLTP activity inversely correlates with CAAD: effects of PON1 enzyme activity and genetic variants on PLTP activity.	Kim DS	J Lipid Res
21736953	Role of plasma phospholipid transfer protein in lipid and lipoprotein metabolism.	Albers JJ	Biochim Biophys Acta
19965587	Genetic and nongenetic sources of variation in phospholipid transfer protein activity.	Jarvik GP	J Lipid Res
21041806	Genetic determinants of plasma triglycerides.	Johansen CT	J Lipid Res
22315312	Genetic predisposition to dyslipidemia and type 2 diabetes risk in two prospective cohorts.	Qi Q	Diabetes
22629316	Multi-ethnic analysis of lipid-associated loci: the NHLBI CARe project.	Musunuru K	PLoS One

SNP ID	p-value	Traits	Study
rs4810479	0.000333	alcohol dependence	20201924

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

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 )
chr20	44518515	44518565	E067	-26483
chr20	44521405	44522134	E067	-22914
chr20	44512367	44512655	E068	-32393
chr20	44512699	44512947	E068	-32101
chr20	44518212	44518330	E068	-26718
chr20	44518515	44518565	E068	-26483
chr20	44538189	44538281	E068	-6767
chr20	44538322	44538403	E068	-6645
chr20	44538499	44538988	E068	-6060
chr20	44541501	44541556	E068	-3492
chr20	44547447	44547608	E068	2399
chr20	44547632	44547877	E068	2584
chr20	44547991	44548082	E068	2943
chr20	44548189	44549428	E068	3141
chr20	44549522	44549716	E068	4474
chr20	44549761	44549945	E068	4713
chr20	44550081	44550192	E068	5033
chr20	44550437	44550505	E068	5389
chr20	44550508	44550682	E068	5460
chr20	44550761	44550842	E068	5713
chr20	44553072	44553559	E068	8024
chr20	44510608	44510658	E069	-34390
chr20	44510800	44510882	E069	-34166
chr20	44510937	44510983	E069	-34065
chr20	44552853	44552919	E069	7805
chr20	44553072	44553559	E069	8024
chr20	44509063	44509168	E070	-35880
chr20	44509193	44509278	E070	-35770
chr20	44518515	44518565	E070	-26483
chr20	44521405	44522134	E070	-22914
chr20	44522332	44522435	E070	-22613
chr20	44522436	44522551	E070	-22497
chr20	44555336	44555762	E070	10288
chr20	44565587	44565650	E070	20539
chr20	44565820	44565947	E070	20772
chr20	44566007	44566248	E070	20959
chr20	44510800	44510882	E071	-34166
chr20	44510937	44510983	E071	-34065
chr20	44538322	44538403	E071	-6645
chr20	44538499	44538988	E071	-6060
chr20	44546390	44546731	E071	1342
chr20	44546785	44547407	E071	1737
chr20	44547447	44547608	E071	2399
chr20	44547632	44547877	E071	2584
chr20	44547991	44548082	E071	2943
chr20	44548189	44549428	E071	3141
chr20	44553072	44553559	E071	8024
chr20	44564870	44564932	E071	19822
chr20	44565105	44565224	E071	20057
chr20	44565255	44565355	E071	20207
chr20	44565396	44565582	E071	20348
chr20	44565587	44565650	E071	20539
chr20	44565820	44565947	E071	20772
chr20	44566007	44566248	E071	20959
chr20	44566400	44566749	E071	21352
chr20	44566865	44566951	E071	21817
chr20	44567048	44567098	E071	22000
chr20	44512699	44512947	E072	-32101
chr20	44538322	44538403	E072	-6645
chr20	44538499	44538988	E072	-6060
chr20	44546785	44547407	E072	1737
chr20	44553672	44553819	E072	8624
chr20	44553964	44554112	E072	8916
chr20	44566400	44566749	E072	21352
chr20	44510608	44510658	E073	-34390
chr20	44510800	44510882	E073	-34166
chr20	44510937	44510983	E073	-34065
chr20	44512021	44512118	E073	-32930
chr20	44512172	44512231	E073	-32817
chr20	44512263	44512330	E073	-32718
chr20	44512367	44512655	E073	-32393
chr20	44513585	44514088	E073	-30960
chr20	44521405	44522134	E073	-22914
chr20	44538499	44538988	E073	-6060
chr20	44546390	44546731	E073	1342
chr20	44546785	44547407	E073	1737
chr20	44548189	44549428	E073	3141
chr20	44550437	44550505	E073	5389
chr20	44550508	44550682	E073	5460
chr20	44551150	44551467	E073	6102
chr20	44566007	44566248	E073	20959
chr20	44566400	44566749	E073	21352
chr20	44503124	44503446	E074	-41602
chr20	44549522	44549716	E074	4474
chr20	44552853	44552919	E074	7805
chr20	44553072	44553559	E074	8024
chr20	44564870	44564932	E074	19822
chr20	44510608	44510658	E081	-34390
chr20	44510800	44510882	E081	-34166
chr20	44510937	44510983	E081	-34065
chr20	44512367	44512655	E081	-32393
chr20	44512699	44512947	E081	-32101
chr20	44538020	44538158	E081	-6890
chr20	44538189	44538281	E081	-6767
chr20	44538322	44538403	E081	-6645
chr20	44538499	44538988	E081	-6060
chr20	44553072	44553559	E081	8024
chr20	44561592	44561746	E081	16544
chr20	44511205	44511628	E082	-33420
chr20	44511702	44511837	E082	-33211
chr20	44511846	44511886	E082	-33162
chr20	44511906	44511975	E082	-33073
chr20	44512021	44512118	E082	-32930
chr20	44512172	44512231	E082	-32817
chr20	44512263	44512330	E082	-32718
chr20	44512367	44512655	E082	-32393
chr20	44517482	44517722	E082	-27326
chr20	44517726	44517946	E082	-27102
chr20	44518515	44518565	E082	-26483

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	44509448	44510451	E067	-34597
chr20	44518604	44521322	E067	-23726
chr20	44539088	44541437	E067	-3611
chr20	44561763	44564769	E067	16715
chr20	44509448	44510451	E068	-34597
chr20	44518604	44521322	E068	-23726
chr20	44539088	44541437	E068	-3611
chr20	44561763	44564769	E068	16715
chr20	44509448	44510451	E069	-34597
chr20	44518604	44521322	E069	-23726
chr20	44539088	44541437	E069	-3611
chr20	44561763	44564769	E069	16715
chr20	44509448	44510451	E070	-34597
chr20	44518604	44521322	E070	-23726
chr20	44539088	44541437	E070	-3611
chr20	44561763	44564769	E070	16715
chr20	44509448	44510451	E071	-34597
chr20	44518604	44521322	E071	-23726
chr20	44539088	44541437	E071	-3611
chr20	44561763	44564769	E071	16715
chr20	44509448	44510451	E072	-34597
chr20	44518604	44521322	E072	-23726
chr20	44539088	44541437	E072	-3611
chr20	44561763	44564769	E072	16715
chr20	44518604	44521322	E073	-23726
chr20	44539088	44541437	E073	-3611
chr20	44561763	44564769	E073	16715
chr20	44509448	44510451	E074	-34597
chr20	44518604	44521322	E074	-23726
chr20	44539088	44541437	E074	-3611
chr20	44561763	44564769	E074	16715
chr20	44509448	44510451	E081	-34597
chr20	44561763	44564769	E081	16715
chr20	44509448	44510451	E082	-34597
chr20	44518604	44521322	E082	-23726
chr20	44539088	44541437	E082	-3611
chr20	44561763	44564769	E082	16715

rs4810479

Genomic Coordinates

Population Frequency

P-Value

eQTL of rs4810479 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs4810479 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)