rs6486717

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

TMEM132C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0426 (12765/29900,GnomAD)
T==0410 (11949/29118,TOPMED)
T==0449 (2248/5008,1000G)
T==0436 (1681/3854,ALSPAC)
T==0434 (1611/3708,TWINSUK)

Position: chr12:128683327 (GRCh38.p7) (12q24.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 63 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.128683327T>G
GRCh37.p13 chr 12	NC_000012.11:g.129167872T>G

Gene: TMEM132C, transmembrane protein 132C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM132C transcript	NM_001136103.2:c.	N/A	Intron Variant
TMEM132C transcript variant X1	XM_011538998.2:c.	N/A	Intron Variant
TMEM132C transcript variant X2	XR_001748922.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.360	G=0.640
1000Genomes	American	Sub	694	T=0.450	G=0.550
1000Genomes	East Asian	Sub	1008	T=0.467	G=0.533
1000Genomes	Europe	Sub	1006	T=0.439	G=0.561
1000Genomes	Global	Study-wide	5008	T=0.449	G=0.551
1000Genomes	South Asian	Sub	978	T=0.560	G=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.436	G=0.564
The Genome Aggregation Database	African	Sub	8708	T=0.376	G=0.624
The Genome Aggregation Database	American	Sub	838	T=0.450	G=0.550
The Genome Aggregation Database	East Asian	Sub	1614	T=0.485	G=0.515
The Genome Aggregation Database	Europe	Sub	18438	T=0.444	G=0.555
The Genome Aggregation Database	Global	Study-wide	29900	T=0.426	G=0.573
The Genome Aggregation Database	Other	Sub	302	T=0.440	G=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.410	G=0.589
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.434	G=0.566

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
rs6486717	0.0000689	alcoholism	pha002893
rs6486717	0.000069	alcohol dependence	20201924
rs6486717	0.00024	alcohol dependence(early age of onset)	20201924

eQTL of rs6486717 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 rs6486717 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 )
chr12	129136834	129136874	E067	-30998
chr12	129169006	129169234	E067	1134
chr12	129169242	129169363	E067	1370
chr12	129169485	129169535	E067	1613
chr12	129176616	129176696	E067	8744
chr12	129176885	129176945	E067	9013
chr12	129199266	129199327	E067	31394
chr12	129169006	129169234	E068	1134
chr12	129169242	129169363	E068	1370
chr12	129169485	129169535	E068	1613
chr12	129169673	129169723	E068	1801
chr12	129127406	129127495	E069	-40377
chr12	129127653	129127861	E069	-40011
chr12	129127892	129128114	E069	-39758
chr12	129136834	129136874	E069	-30998
chr12	129138683	129138754	E069	-29118
chr12	129138761	129138821	E069	-29051
chr12	129139125	129139282	E069	-28590
chr12	129145681	129146264	E069	-21608
chr12	129169006	129169234	E069	1134
chr12	129169242	129169363	E069	1370
chr12	129169485	129169535	E069	1613
chr12	129169673	129169723	E069	1801
chr12	129175392	129175442	E069	7520
chr12	129136834	129136874	E070	-30998
chr12	129138761	129138821	E070	-29051
chr12	129139125	129139282	E070	-28590
chr12	129144617	129144691	E070	-23181
chr12	129144929	129145350	E070	-22522
chr12	129145681	129146264	E070	-21608
chr12	129146497	129146687	E070	-21185
chr12	129146715	129146969	E070	-20903
chr12	129147088	129147275	E070	-20597
chr12	129127406	129127495	E071	-40377
chr12	129127892	129128114	E071	-39758
chr12	129134540	129134618	E071	-33254
chr12	129134677	129134726	E071	-33146
chr12	129137551	129137601	E071	-30271
chr12	129137796	129137874	E071	-29998
chr12	129137897	129137947	E071	-29925
chr12	129138155	129138249	E071	-29623
chr12	129169006	129169234	E071	1134
chr12	129169242	129169363	E071	1370
chr12	129169485	129169535	E071	1613
chr12	129169673	129169723	E071	1801
chr12	129200078	129200279	E071	32206
chr12	129136834	129136874	E072	-30998
chr12	129137551	129137601	E072	-30271
chr12	129138761	129138821	E072	-29051
chr12	129169006	129169234	E072	1134
chr12	129169242	129169363	E072	1370
chr12	129169006	129169234	E073	1134
chr12	129169242	129169363	E073	1370
chr12	129169485	129169535	E073	1613
chr12	129172475	129172620	E073	4603
chr12	129172745	129172795	E073	4873
chr12	129169006	129169234	E074	1134
chr12	129169242	129169363	E074	1370
chr12	129169485	129169535	E074	1613
chr12	129127892	129128114	E081	-39758
chr12	129145681	129146264	E081	-21608
chr12	129169006	129169234	E081	1134
chr12	129183532	129183605	E081	15660