rs3762317

Organism: Homo sapiens

Alleles: A>C / A>G

Gene : Feature

IL12RB2 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0218 (6539/29910,GnomAD)
G=0271 (7893/29118,TOPMED)
G=0255 (1276/5008,1000G)
G=0126 (486/3854,ALSPAC)
G=0131 (487/3708,TWINSUK)

Position: chr1:67306899 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.67306899A>C
GRCh38.p7 chr 1	NC_000001.11:g.67306899A>G
GRCh37.p13 chr 1	NC_000001.10:g.67772582A>C
GRCh37.p13 chr 1	NC_000001.10:g.67772582A>G
IL12RB2 RefSeqGene	NG_032977.1:g.4536A>C
IL12RB2 RefSeqGene	NG_032977.1:g.4536A>G

Gene: IL12RB2, interleukin 12 receptor subunit beta 2(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
IL12RB2 transcript variant 2	NM_001258214.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 3	NM_001258215.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 4	NM_001258216.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 7	NM_001319233.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 1	NM_001559.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 5	NR_047583.1:n.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant 6	NR_047584.1:n.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X1	XM_005270825.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X3	XM_005270827.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X4	XM_005270828.3:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X6	XM_006710617.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X2	XM_011541383.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X5	XM_011541384.2:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X7	XM_017001202.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X7	XM_017001203.1:c.	N/A	Upstream Transcript Variant
IL12RB2 transcript variant X8	XM_017001204.1:c.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.523	G=0.477
1000Genomes	American	Sub	694	A=0.760	G=0.240
1000Genomes	East Asian	Sub	1008	A=0.818	G=0.182
1000Genomes	Europe	Sub	1006	A=0.858	G=0.142
1000Genomes	Global	Study-wide	5008	A=0.745	G=0.255
1000Genomes	South Asian	Sub	978	A=0.840	G=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.874	G=0.126
The Genome Aggregation Database	African	Sub	8692	A=0.555	G=0.445
The Genome Aggregation Database	American	Sub	836	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1620	A=0.851	G=0.149
The Genome Aggregation Database	Europe	Sub	18460	A=0.878	G=0.121
The Genome Aggregation Database	Global	Study-wide	29910	A=0.781	G=0.218
The Genome Aggregation Database	Other	Sub	302	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.728	G=0.271
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.869	G=0.131

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
20525402	Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis: a case-control association study.	Moller M	BMC Infect Dis

P-Value

SNP ID	p-value	Traits	Study
rs3762317	0.00084	alcohol dependence	20201924

eQTL of rs3762317 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 rs3762317 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 )
chr1	111817394	111817664	E068	-35917
chr1	111817762	111818087	E068	-35494
chr1	111814880	111814951	E070	-38630
chr1	111817394	111817664	E071	-35917
chr1	111817762	111818087	E071	-35494
chr1	111817394	111817664	E072	-35917
chr1	111817394	111817664	E074	-35917
chr1	111817762	111818087	E074	-35494

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111888671	111889542	E067	35090
chr1	111889571	111889663	E067	35990
chr1	111888671	111889542	E068	35090
chr1	111889571	111889663	E068	35990
chr1	111888671	111889542	E069	35090
chr1	111889571	111889663	E069	35990
chr1	111888671	111889542	E070	35090
chr1	111889571	111889663	E070	35990
chr1	111888671	111889542	E071	35090
chr1	111889571	111889663	E071	35990
chr1	111888671	111889542	E072	35090
chr1	111889571	111889663	E072	35990
chr1	111888671	111889542	E073	35090
chr1	111889571	111889663	E073	35990
chr1	111888671	111889542	E074	35090
chr1	111889571	111889663	E074	35990
chr1	111888671	111889542	E082	35090