SNP Detail Info-rs116439821

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.202215693C>T
GRCh37.p13 chr 1	NC_000001.10:g.202184821C>T

Gene: LGR6, leucine-rich repeat containing G protein-coupled receptor 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LGR6 transcript variant 1	NM_001017403.1:c.	N/A	Intron Variant
LGR6 transcript variant 3	NM_001017404.1:c.	N/A	Intron Variant
LGR6 transcript variant 2	NM_021636.2:c.	N/A	Intron Variant
LGR6 transcript variant X1	XM_005245404.3:c.	N/A	Intron Variant
LGR6 transcript variant X2	XM_011509838.2:c.	N/A	Intron Variant
LGR6 transcript variant X3	XM_011509839.2:c.	N/A	Intron Variant
LGR6 transcript variant X5	XM_011509840.2:c.	N/A	Intron Variant
LGR6 transcript variant X4	XM_017001996.1:c.	N/A	Intron Variant
LGR6 transcript variant X7	XM_011509841.2:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X8	XM_011509842.2:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X9	XM_011509843.2:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X10	XM_011509844.2:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X11	XM_011509846.2:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X6	XM_017001997.1:c.	N/A	Genic Upstream Transcript Variant
LGR6 transcript variant X12	XM_017001998.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.950	T=0.050
1000Genomes	American	Sub	694	C=1.000	T=0.000
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.986	T=0.014
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=1.000	T=0.000
The Genome Aggregation Database	African	Sub	8722	C=0.961	T=0.039
The Genome Aggregation Database	American	Sub	838	C=1.000	T=0.000
The Genome Aggregation Database	East Asian	Sub	1622	C=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18492	C=0.999	T=0.000
The Genome Aggregation Database	Global	Study-wide	29976	C=0.988	T=0.011
The Genome Aggregation Database	Other	Sub	302	C=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.980	T=0.020
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=1.000	T=0.000

PMID	Title	Author	Journal
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs116439821	1.55E-05	cocaine dependence	23958962

eQTL of rs116439821 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 rs116439821 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 )
chr1	202153772	202154287	E067	-30534
chr1	202153772	202154287	E068	-30534
chr1	202154307	202154441	E068	-30380
chr1	202156117	202156818	E068	-28003
chr1	202185928	202185992	E068	1107
chr1	202186060	202186182	E068	1239
chr1	202186830	202186891	E068	2009
chr1	202190809	202191251	E068	5988
chr1	202218799	202218925	E068	33978
chr1	202219134	202219228	E068	34313
chr1	202153772	202154287	E069	-30534
chr1	202154307	202154441	E069	-30380
chr1	202190809	202191251	E069	5988
chr1	202136882	202137028	E070	-47793
chr1	202137065	202137547	E070	-47274
chr1	202218799	202218925	E070	33978
chr1	202219134	202219228	E070	34313
chr1	202185928	202185992	E071	1107
chr1	202190809	202191251	E071	5988
chr1	202191366	202191870	E071	6545
chr1	202154307	202154441	E072	-30380
chr1	202156117	202156818	E072	-28003
chr1	202190809	202191251	E072	5988
chr1	202216932	202217216	E072	32111
chr1	202217454	202217820	E072	32633
chr1	202218579	202218745	E072	33758
chr1	202218799	202218925	E072	33978
chr1	202219134	202219228	E072	34313
chr1	202186060	202186182	E073	1239
chr1	202136882	202137028	E081	-47793
chr1	202137065	202137547	E081	-47274
chr1	202137666	202137781	E081	-47040
chr1	202138181	202138240	E081	-46581
chr1	202138535	202138595	E081	-46226
chr1	202153772	202154287	E081	-30534
chr1	202191366	202191870	E081	6545
chr1	202192392	202192638	E081	7571
chr1	202192775	202192884	E081	7954
chr1	202218579	202218745	E081	33758
chr1	202218799	202218925	E081	33978
chr1	202219134	202219228	E081	34313
chr1	202136882	202137028	E082	-47793
chr1	202137065	202137547	E082	-47274
chr1	202184589	202184671	E082	-150
chr1	202184719	202184769	E082	-52
chr1	202184771	202184856	E082	0
chr1	202192392	202192638	E082	7571
chr1	202192775	202192884	E082	7954
chr1	202218579	202218745	E082	33758
chr1	202218799	202218925	E082	33978
chr1	202219134	202219228	E082	34313

rs116439821

Genomic Coordinates

Gene: LGR6, leucine-rich repeat containing G protein-coupled receptor 6(plus strand)

Population Frequency

P-Value

eQTL of rs116439821 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs116439821 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	202183195	202183737	E069	-1084
chr1	202183195	202183737	E082	-1084