rs3826878

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

KIR3DL2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0041 (1240/29954,GnomAD)
G=0043 (1264/29118,TOPMED)
A==0041 (539/13006,GO-ESP)
G=0051 (256/5008,1000G)

Position: chr19:54865756 (GRCh38.p7) (19q13.42)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 23 Enhancers around

Promoter: 33 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.54865756A>G
GRCh38.p7 chr 19	NC_000019.10:g.54865756A>T
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.840124A>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.840124A>T
KIR3DL2 RefSeqGene	NG_012802.1:g.20314A>G
KIR3DL2 RefSeqGene	NG_012802.1:g.20314A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.847696A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_S_CTG3_1	NW_003571058.2:g.847696A>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_LRC_S_CTG1	NW_003571058.1:g.847695A>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_LRC_S_CTG1	NW_003571058.1:g.847695A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.784346A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_LRC_T_CTG3_1	NW_003571059.2:g.784346A>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_LRC_T_CTG1	NW_003571059.1:g.784345A>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_LRC_T_CTG1	NW_003571059.1:g.784345A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.511030A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX2_CTG3_1	NW_003571055.2:g.511030A>T
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.511029A>G
GRCh37.p13 chr 19 novel patch HSCHR19LRC_COX2_CTG1	NW_003571055.1:g.511029A>T
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.848325A>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.848325A>T
GRCh37.p13 chr 19	NC_000019.9:g.55377211A>G
GRCh37.p13 chr 19	NC_000019.9:g.55377211A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH06_A_HAP_CTG3_1	NT_187676.1:g.141706A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH06_A_HAP_CTG3_1	NT_187676.1:g.141706A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH06_BA1_HAP_CTG3_1	NT_187677.1:g.143122A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH06_BA1_HAP_CTG3_1	NT_187677.1:g.143122A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH13_A_HAP_CTG3_1	NT_187685.1:g.3658T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH13_A_HAP_CTG3_1	NT_187685.1:g.3658T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH05_A_HAP_CTG3_1	NT_187674.1:g.151780A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH05_A_HAP_CTG3_1	NT_187674.1:g.151780A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH05_B_HAP_CTG3_1	NT_187675.1:g.235995A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH05_B_HAP_CTG3_1	NT_187675.1:g.235995A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH13_BA2_HAP_CTG3_1	NT_187686.1:g.3636T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH13_BA2_HAP_CTG3_1	NT_187686.1:g.3636T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_GRC212_AB_HAP_CTG3_1	NT_187641.1:g.15431T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_GRC212_AB_HAP_CTG3_1	NT_187641.1:g.15431T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_T7526_BDEL_HAP_CTG3_1	NT_187670.1:g.3543T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_T7526_BDEL_HAP_CTG3_1	NT_187670.1:g.3543T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH15_B_HAP_CTG3_1	NT_187636.1:g.9756T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH15_B_HAP_CTG3_1	NT_187636.1:g.9756T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_ABC08_A1_HAP_CTG3_1	NT_187671.1:g.144703A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_ABC08_A1_HAP_CTG3_1	NT_187671.1:g.144703A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH08_A_HAP_CTG3_1	NT_187683.1:g.139975A>G
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH08_A_HAP_CTG3_1	NT_187683.1:g.139975A>T
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.770131A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.770131A>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G248_A_HAP_CTG3_1	NT_187639.1:g.3610T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G248_A_HAP_CTG3_1	NT_187639.1:g.3610T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH08_BAX_HAP_CTG3_1	NT_187684.1:g.3301T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH08_BAX_HAP_CTG3_1	NT_187684.1:g.3301T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1	NT_187673.1:g.3302T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1	NT_187673.1:g.3302T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH15_A_HAP_CTG3_1	NT_187687.1:g.3301T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_FH15_A_HAP_CTG3_1	NT_187687.1:g.3301T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_RSH_A_HAP_CTG3_1	NT_187645.1:g.3301T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_RSH_A_HAP_CTG3_1	NT_187645.1:g.3301T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1	NT_187644.1:g.3290T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1	NT_187644.1:g.3290T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_T7526_A_HAP_CTG3_1	NT_187669.1:g.3301T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_T7526_A_HAP_CTG3_1	NT_187669.1:g.3301T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_LUCE_A_HAP_CTG3_1	NT_187643.1:g.3301T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_LUCE_A_HAP_CTG3_1	NT_187643.1:g.3301T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_GRC212_BA1_HAP_CTG3_1	NT_187642.1:g.3174T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_GRC212_BA1_HAP_CTG3_1	NT_187642.1:g.3174T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G085_A_HAP_CTG3_1	NT_187637.1:g.3035T>C
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G085_A_HAP_CTG3_1	NT_187637.1:g.3035T>A
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G085_BA1_HAP_CTG3_1	NT_187638.1:g.3484C>T
GRCh38.p7 chr 19 alt locus HSCHR19KIR_G085_BA1_HAP_CTG3_1	NT_187638.1:g.3484C>A

Gene: KIR3DL2, killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KIR3DL2 transcript variant 2	NM_001242867.1:c.	N/A	Intron Variant
KIR3DL2 transcript variant 1	NM_006737.3:c.	N/A	Intron Variant
KIR3DL2 transcript variant X1	XM_011526940.2:c.	N/A	Intron Variant
KIR3DL2 transcript variant X2	XM_017026784.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.953	G=0.047
1000Genomes	American	Sub	694	A=0.970	G=0.030
1000Genomes	East Asian	Sub	1008	A=0.912	G=0.088
1000Genomes	Europe	Sub	1006	A=0.961	G=0.039
1000Genomes	Global	Study-wide	5008	A=0.949	G=0.051
1000Genomes	South Asian	Sub	978	A=0.950	G=0.050
The Genome Aggregation Database	African	Sub	8726	A=0.941	T=0.000
The Genome Aggregation Database	American	Sub	838	A=0.970	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1620	A=0.914	T=0.000
The Genome Aggregation Database	Europe	Sub	18468	A=0.970	T=0.000
The Genome Aggregation Database	Global	Study-wide	29954	A=0.958	T=0.000
The Genome Aggregation Database	Other	Sub	302	A=0.960	T=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.956	G=0.043

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs3826878	2E-05	alcohol dependence	24277619

eQTL of rs3826878 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 rs3826878 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	33764873	33765572	E067	-28980
chr19	33764873	33765572	E068	-28980
chr19	33783383	33785493	E068	-9059
chr19	33807341	33808220	E068	12789
chr19	33752394	33752482	E069	-42070
chr19	33752518	33752674	E069	-41878
chr19	33752799	33752849	E069	-41703
chr19	33764873	33765572	E069	-28980
chr19	33764254	33764840	E071	-29712
chr19	33764873	33765572	E071	-28980
chr19	33768907	33769071	E071	-25481
chr19	33769166	33769216	E071	-25336
chr19	33770423	33770512	E071	-24040
chr19	33770782	33770909	E071	-23643
chr19	33770926	33771071	E071	-23481
chr19	33771206	33771273	E071	-23279
chr19	33776218	33776309	E071	-18243
chr19	33821452	33821558	E071	26900
chr19	33764873	33765572	E072	-28980
chr19	33764873	33765572	E073	-28980
chr19	33783383	33785493	E074	-9059
chr19	33783383	33785493	E081	-9059
chr19	33783383	33785493	E082	-9059

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	33790247	33792599	E067	-1953
chr19	33792654	33792741	E067	-1811
chr19	33792776	33792893	E067	-1659
chr19	33792930	33795456	E067	0
chr19	33790247	33792599	E068	-1953
chr19	33792654	33792741	E068	-1811
chr19	33792776	33792893	E068	-1659
chr19	33792930	33795456	E068	0
chr19	33790247	33792599	E069	-1953
chr19	33792654	33792741	E069	-1811
chr19	33792776	33792893	E069	-1659
chr19	33792930	33795456	E069	0
chr19	33792654	33792741	E070	-1811
chr19	33792776	33792893	E070	-1659
chr19	33790247	33792599	E071	-1953
chr19	33792654	33792741	E071	-1811
chr19	33792776	33792893	E071	-1659
chr19	33792930	33795456	E071	0
chr19	33790247	33792599	E072	-1953
chr19	33792654	33792741	E072	-1811
chr19	33792776	33792893	E072	-1659
chr19	33792930	33795456	E072	0
chr19	33790247	33792599	E073	-1953
chr19	33792654	33792741	E073	-1811
chr19	33792776	33792893	E073	-1659
chr19	33792930	33795456	E073	0
chr19	33790247	33792599	E074	-1953
chr19	33792654	33792741	E074	-1811
chr19	33792776	33792893	E074	-1659
chr19	33792930	33795456	E074	0
chr19	33792654	33792741	E082	-1811
chr19	33792776	33792893	E082	-1659
chr19	33792930	33795456	E082	0