rs1979522

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LRMP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0082 (2471/29960,GnomAD)
T=0074 (2168/29118,TOPMED)
T=0073 (368/5008,1000G)
T=0105 (406/3854,ALSPAC)
T=0111 (410/3708,TWINSUK)

Position: chr12:25090959 (GRCh38.p7) (12p12.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 13 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.25090959C>T
GRCh37.p13 chr 12	NC_000012.11:g.25243893C>T

Gene: LRMP, lymphoid restricted membrane protein(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRMP transcript variant 2	NM_001204126.1:c.	N/A	Intron Variant
LRMP transcript variant 3	NM_001204127.1:c.	N/A	Intron Variant
LRMP transcript variant 1	NM_006152.3:c.	N/A	Intron Variant
LRMP transcript variant X2	XM_005253370.3:c.	N/A	Intron Variant
LRMP transcript variant X4	XM_005253372.2:c.	N/A	Intron Variant
LRMP transcript variant X7	XM_005253374.3:c.	N/A	Intron Variant
LRMP transcript variant X8	XM_006719076.2:c.	N/A	Intron Variant
LRMP transcript variant X1	XM_011520667.1:c.	N/A	Intron Variant
LRMP transcript variant X10	XM_011520668.2:c.	N/A	Intron Variant
LRMP transcript variant X9	XM_011520669.2:c.	N/A	Intron Variant
LRMP transcript variant X11	XM_011520670.1:c.	N/A	Intron Variant
LRMP transcript variant X3	XM_017019300.1:c.	N/A	Intron Variant
LRMP transcript variant X5	XM_017019301.1:c.	N/A	Intron Variant
LRMP transcript variant X6	XM_017019302.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.933	T=0.067
1000Genomes	American	Sub	694	C=0.950	T=0.050
1000Genomes	East Asian	Sub	1008	C=0.993	T=0.007
1000Genomes	Europe	Sub	1006	C=0.905	T=0.095
1000Genomes	Global	Study-wide	5008	C=0.927	T=0.073
1000Genomes	South Asian	Sub	978	C=0.850	T=0.150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.895	T=0.105
The Genome Aggregation Database	African	Sub	8716	C=0.922	T=0.078
The Genome Aggregation Database	American	Sub	836	C=0.950	T=0.050
The Genome Aggregation Database	East Asian	Sub	1620	C=0.991	T=0.009
The Genome Aggregation Database	Europe	Sub	18486	C=0.907	T=0.093
The Genome Aggregation Database	Global	Study-wide	29960	C=0.917	T=0.082
The Genome Aggregation Database	Other	Sub	302	C=0.940	T=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.925	T=0.074
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.889	T=0.111

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs1979522	4.38E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs1979522 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 rs1979522 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.

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	25207002	25208271	E067	-35622
chr12	25207002	25208271	E068	-35622
chr12	25207002	25208271	E069	-35622
chr12	25206256	25206306	E071	-37587
chr12	25206391	25206470	E071	-37423
chr12	25206594	25206644	E071	-37249
chr12	25206760	25206906	E071	-36987
chr12	25207002	25208271	E071	-35622
chr12	25206256	25206306	E072	-37587
chr12	25206391	25206470	E072	-37423
chr12	25206594	25206644	E072	-37249
chr12	25206760	25206906	E072	-36987
chr12	25207002	25208271	E072	-35622