SNP Detail Info-rs7612780

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

OSBPL10 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0214 (6421/29926,GnomAD)
A==0227 (6614/29118,TOPMED)
A==0215 (1077/5008,1000G)
A==0227 (874/3854,ALSPAC)
A==0234 (866/3708,TWINSUK)

Position: chr3:31769066 (GRCh38.p7) (3p23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 52 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.31769066A>G
GRCh37.p13 chr 3	NC_000003.11:g.31810558A>G

Gene: OSBPL10, oxysterol binding protein like 10(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OSBPL10 transcript variant 2	NM_001174060.1:c.	N/A	Intron Variant
OSBPL10 transcript variant 1	NM_017784.4:c.	N/A	Intron Variant
OSBPL10 transcript variant X1	XM_005264843.3:c.	N/A	Intron Variant
OSBPL10 transcript variant X2	XM_005264844.4:c.	N/A	Intron Variant
OSBPL10 transcript variant X3	XM_011533326.2:c.	N/A	Intron Variant
OSBPL10 transcript variant X3	XM_017005667.1:c.	N/A	Intron Variant
OSBPL10 transcript variant X4	XM_017005668.1:c.	N/A	Intron Variant
OSBPL10 transcript variant X6	XM_017005669.1:c.	N/A	Intron Variant
OSBPL10 transcript variant X7	XM_017005670.1:c.	N/A	Intron Variant
OSBPL10 transcript variant X5	XM_005264845.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.207	G=0.793
1000Genomes	American	Sub	694	A=0.230	G=0.770
1000Genomes	East Asian	Sub	1008	A=0.188	G=0.812
1000Genomes	Europe	Sub	1006	A=0.214	G=0.786
1000Genomes	Global	Study-wide	5008	A=0.215	G=0.785
1000Genomes	South Asian	Sub	978	A=0.250	G=0.750
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.227	G=0.773
The Genome Aggregation Database	African	Sub	8704	A=0.208	G=0.792
The Genome Aggregation Database	American	Sub	834	A=0.230	G=0.770
The Genome Aggregation Database	East Asian	Sub	1618	A=0.192	G=0.808
The Genome Aggregation Database	Europe	Sub	18468	A=0.218	G=0.781
The Genome Aggregation Database	Global	Study-wide	29926	A=0.214	G=0.785
The Genome Aggregation Database	Other	Sub	302	A=0.260	G=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.227	G=0.772
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.234	G=0.766

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
rs7612780	0.00081	alcohol dependence	20201924

eQTL of rs7612780 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 rs7612780 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	31774078	31774256	E070	-36302
chr3	31774530	31775104	E070	-35454
chr3	31831131	31831223	E070	20573
chr3	31831523	31832941	E070	20965
chr3	31833003	31833108	E070	22445
chr3	31765756	31765931	E081	-44627
chr3	31765948	31766161	E081	-44397
chr3	31766187	31766458	E081	-44100
chr3	31774078	31774256	E081	-36302
chr3	31774530	31775104	E081	-35454
chr3	31795738	31795910	E081	-14648
chr3	31796127	31796281	E081	-14277
chr3	31799913	31799963	E081	-10595
chr3	31799978	31800101	E081	-10457
chr3	31800175	31800255	E081	-10303
chr3	31804282	31804565	E081	-5993
chr3	31805267	31805334	E081	-5224
chr3	31805592	31805676	E081	-4882
chr3	31805748	31805857	E081	-4701
chr3	31813407	31813457	E081	2849
chr3	31813504	31813573	E081	2946
chr3	31814092	31814167	E081	3534
chr3	31814290	31814534	E081	3732
chr3	31814568	31814869	E081	4010
chr3	31831131	31831223	E081	20573
chr3	31831523	31832941	E081	20965
chr3	31833003	31833108	E081	22445
chr3	31833399	31833477	E081	22841
chr3	31833715	31833877	E081	23157
chr3	31834129	31834509	E081	23571
chr3	31834677	31834821	E081	24119
chr3	31835446	31835620	E081	24888
chr3	31835868	31835918	E081	25310
chr3	31836386	31836456	E081	25828
chr3	31774078	31774256	E082	-36302
chr3	31774530	31775104	E082	-35454
chr3	31795738	31795910	E082	-14648
chr3	31796127	31796281	E082	-14277
chr3	31805267	31805334	E082	-5224
chr3	31805592	31805676	E082	-4882
chr3	31805748	31805857	E082	-4701
chr3	31814092	31814167	E082	3534
chr3	31814290	31814534	E082	3732
chr3	31814568	31814869	E082	4010
chr3	31831131	31831223	E082	20573
chr3	31831523	31832941	E082	20965
chr3	31833003	31833108	E082	22445
chr3	31833399	31833477	E082	22841
chr3	31833715	31833877	E082	23157
chr3	31834129	31834509	E082	23571
chr3	31834677	31834821	E082	24119
chr3	31835446	31835620	E082	24888

rs7612780