rs6712333

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SP140L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0260 (7770/29790,GnomAD)
T=0304 (8871/29118,TOPMED)
T=0402 (2015/5008,1000G)
T=0121 (468/3854,ALSPAC)
T=0115 (428/3708,TWINSUK)

Position: chr2:230365456 (GRCh38.p7) (2q37.1)

Phenotype: AD | ND

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.230365456C>T
GRCh37.p13 chr 2	NC_000002.11:g.231230171C>T

Gene: SP140L, SP140 nuclear body protein like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SP140L transcript variant 2	NM_001308162.1:c.	N/A	Intron Variant
SP140L transcript variant 3	NM_001308163.1:c.	N/A	Intron Variant
SP140L transcript variant 1	NM_138402.4:c.	N/A	Intron Variant
SP140L transcript variant X8	XM_006712855.2:c.	N/A	Intron Variant
SP140L transcript variant X7	XM_006712856.2:c.	N/A	Intron Variant
SP140L transcript variant X10	XM_006712858.3:c.	N/A	Intron Variant
SP140L transcript variant X12	XM_011512190.2:c.	N/A	Intron Variant
SP140L transcript variant X13	XM_011512191.1:c.	N/A	Intron Variant
SP140L transcript variant X1	XM_017005294.1:c.	N/A	Intron Variant
SP140L transcript variant X2	XM_017005295.1:c.	N/A	Intron Variant
SP140L transcript variant X3	XM_017005296.1:c.	N/A	Intron Variant
SP140L transcript variant X4	XM_017005297.1:c.	N/A	Intron Variant
SP140L transcript variant X5	XM_017005298.1:c.	N/A	Intron Variant
SP140L transcript variant X6	XM_017005299.1:c.	N/A	Intron Variant
SP140L transcript variant X7	XM_017005300.1:c.	N/A	Intron Variant
SP140L transcript variant X15	XM_017005301.1:c.	N/A	Intron Variant
SP140L transcript variant X9	XR_001739075.1:n.	N/A	Intron Variant
SP140L transcript variant X14	XR_001739076.1:n.	N/A	Intron Variant
SP140L transcript variant X11	XR_923066.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.485	T=0.515
1000Genomes	American	Sub	694	C=0.620	T=0.380
1000Genomes	East Asian	Sub	1008	C=0.444	T=0.556
1000Genomes	Europe	Sub	1006	C=0.870	T=0.130
1000Genomes	Global	Study-wide	5008	C=0.598	T=0.402
1000Genomes	South Asian	Sub	978	C=0.610	T=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.879	T=0.121
The Genome Aggregation Database	African	Sub	8688	C=0.518	T=0.482
The Genome Aggregation Database	American	Sub	836	C=0.570	T=0.430
The Genome Aggregation Database	East Asian	Sub	1610	C=0.427	T=0.573
The Genome Aggregation Database	Europe	Sub	18354	C=0.876	T=0.123
The Genome Aggregation Database	Global	Study-wide	29790	C=0.739	T=0.260
The Genome Aggregation Database	Other	Sub	302	C=0.870	T=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.695	T=0.304
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.885	T=0.115

PMID	Title	Author	Journal
23942779	A genome-wide association study of behavioral disinhibition.	McGue M	Behav Genet

P-Value

SNP ID	p-value	Traits	Study
rs6712333	0.000005	nicotine use	23942779
rs6712333	0.000061	alcohol dependence	23942779

eQTL of rs6712333 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 rs6712333 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 )
chr2	231274886	231274936	E067	44715
chr2	231277440	231277610	E068	47269
chr2	231277727	231277913	E068	47556
chr2	231274294	231274458	E071	44123
chr2	231274580	231274694	E071	44409
chr2	231274886	231274936	E071	44715
chr2	231277440	231277610	E074	47269

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	231191480	231192601	E067	-37570
chr2	231275919	231277172	E067	45748
chr2	231191480	231192601	E068	-37570
chr2	231275919	231277172	E068	45748
chr2	231191480	231192601	E069	-37570
chr2	231275919	231277172	E069	45748
chr2	231275919	231277172	E070	45748
chr2	231191480	231192601	E071	-37570
chr2	231275919	231277172	E071	45748
chr2	231191480	231192601	E072	-37570
chr2	231275919	231277172	E072	45748
chr2	231191480	231192601	E073	-37570
chr2	231275919	231277172	E073	45748
chr2	231191480	231192601	E074	-37570
chr2	231275919	231277172	E074	45748
chr2	231275919	231277172	E081	45748
chr2	231275919	231277172	E082	45748