rs12579483

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

TMTC2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0223 (6666/29896,GnomAD)
C=0249 (7271/29118,TOPMED)
C=0329 (1650/5008,1000G)
C=0181 (699/3854,ALSPAC)
C=0183 (680/3708,TWINSUK)

Position: chr12:82695652 (GRCh38.p7) (12q21.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 169 Enhancers around

Promoter: 80 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.82695652T>C
GRCh37.p13 chr 12	NC_000012.11:g.83089431T>C

Gene: TMTC2, transmembrane and tetratricopeptide repeat containing 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMTC2 transcript variant 2	NM_001320321.1:c.	N/A	Intron Variant
TMTC2 transcript variant 3	NM_001320322.1:c.	N/A	Intron Variant
TMTC2 transcript variant 1	NM_152588.2:c.	N/A	Intron Variant
TMTC2 transcript variant X1	XM_017018884.1:c.	N/A	Intron Variant
TMTC2 transcript variant X3	XR_001748601.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.657	C=0.343
1000Genomes	American	Sub	694	T=0.710	C=0.290
1000Genomes	East Asian	Sub	1008	T=0.562	C=0.438
1000Genomes	Europe	Sub	1006	T=0.805	C=0.195
1000Genomes	Global	Study-wide	5008	T=0.671	C=0.329
1000Genomes	South Asian	Sub	978	T=0.640	C=0.360
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.819	C=0.181
The Genome Aggregation Database	African	Sub	8674	T=0.716	C=0.284
The Genome Aggregation Database	American	Sub	834	T=0.750	C=0.250
The Genome Aggregation Database	East Asian	Sub	1606	T=0.553	C=0.447
The Genome Aggregation Database	Europe	Sub	18482	T=0.826	C=0.173
The Genome Aggregation Database	Global	Study-wide	29896	T=0.777	C=0.223
The Genome Aggregation Database	Other	Sub	300	T=0.760	C=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.750	C=0.249
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.817	C=0.183

PMID	Title	Author	Journal
23089632	A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.	Wang JC	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs12579483	1.86E-06	alcohol dependence	23089632

eQTL of rs12579483 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 rs12579483 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	83044267	83045000	E067	-44431
chr12	83084611	83084661	E067	-4770
chr12	83084805	83084859	E067	-4572
chr12	83084895	83084945	E067	-4486
chr12	83085296	83085598	E067	-3833
chr12	83085844	83086057	E067	-3374
chr12	83086451	83086506	E067	-2925
chr12	83092649	83092732	E067	3218
chr12	83101788	83102841	E067	12357
chr12	83126702	83126742	E067	37271
chr12	83127352	83127402	E067	37921
chr12	83138749	83139207	E067	49318
chr12	83139300	83139355	E067	49869
chr12	83044267	83045000	E068	-44431
chr12	83057758	83057933	E068	-31498
chr12	83057947	83058015	E068	-31416
chr12	83075963	83076003	E068	-13428
chr12	83076067	83076422	E068	-13009
chr12	83076551	83076950	E068	-12481
chr12	83085844	83086057	E068	-3374
chr12	83086451	83086506	E068	-2925
chr12	83089427	83089523	E068	0
chr12	83089529	83089650	E068	98
chr12	83089703	83089759	E068	272
chr12	83100599	83100649	E068	11168
chr12	83100694	83100744	E068	11263
chr12	83100939	83101300	E068	11508
chr12	83101396	83101633	E068	11965
chr12	83101788	83102841	E068	12357
chr12	83102895	83102978	E068	13464
chr12	83115014	83115064	E068	25583
chr12	83138749	83139207	E068	49318
chr12	83139300	83139355	E068	49869
chr12	83044267	83045000	E069	-44431
chr12	83053447	83053645	E069	-35786
chr12	83053686	83053817	E069	-35614
chr12	83075641	83075695	E069	-13736
chr12	83075963	83076003	E069	-13428
chr12	83076067	83076422	E069	-13009
chr12	83076551	83076950	E069	-12481
chr12	83084611	83084661	E069	-4770
chr12	83084805	83084859	E069	-4572
chr12	83084895	83084945	E069	-4486
chr12	83092107	83092306	E069	2676
chr12	83092649	83092732	E069	3218
chr12	83092771	83092837	E069	3340
chr12	83101396	83101633	E069	11965
chr12	83101788	83102841	E069	12357
chr12	83102895	83102978	E069	13464
chr12	83103193	83103239	E069	13762
chr12	83103286	83103406	E069	13855
chr12	83103692	83104106	E069	14261
chr12	83114895	83114970	E069	25464
chr12	83115014	83115064	E069	25583
chr12	83138485	83138589	E069	49054
chr12	83138687	83138737	E069	49256
chr12	83138749	83139207	E069	49318
chr12	83139300	83139355	E069	49869
chr12	83075963	83076003	E070	-13428
chr12	83076067	83076422	E070	-13009
chr12	83076551	83076950	E070	-12481
chr12	83084611	83084661	E070	-4770
chr12	83084805	83084859	E070	-4572
chr12	83084895	83084945	E070	-4486
chr12	83085296	83085598	E070	-3833
chr12	83085844	83086057	E070	-3374
chr12	83086451	83086506	E070	-2925
chr12	83101788	83102841	E070	12357
chr12	83125734	83125819	E070	36303
chr12	83126485	83126539	E070	37054
chr12	83126702	83126742	E070	37271
chr12	83127352	83127402	E070	37921
chr12	83138485	83138589	E070	49054
chr12	83138687	83138737	E070	49256
chr12	83138749	83139207	E070	49318
chr12	83139300	83139355	E070	49869
chr12	83041757	83041835	E071	-47596
chr12	83044267	83045000	E071	-44431
chr12	83057758	83057933	E071	-31498
chr12	83057947	83058015	E071	-31416
chr12	83059220	83059363	E071	-30068
chr12	83085844	83086057	E071	-3374
chr12	83088814	83089100	E071	-331
chr12	83089427	83089523	E071	0
chr12	83089529	83089650	E071	98
chr12	83092107	83092306	E071	2676
chr12	83092649	83092732	E071	3218
chr12	83100939	83101300	E071	11508
chr12	83101396	83101633	E071	11965
chr12	83101788	83102841	E071	12357
chr12	83102895	83102978	E071	13464
chr12	83103193	83103239	E071	13762
chr12	83114895	83114970	E071	25464
chr12	83115014	83115064	E071	25583
chr12	83138687	83138737	E071	49256
chr12	83138749	83139207	E071	49318
chr12	83139300	83139355	E071	49869
chr12	83044267	83045000	E072	-44431
chr12	83053686	83053817	E072	-35614
chr12	83057355	83057405	E072	-32026
chr12	83057758	83057933	E072	-31498
chr12	83057947	83058015	E072	-31416
chr12	83066965	83067196	E072	-22235
chr12	83075963	83076003	E072	-13428
chr12	83076067	83076422	E072	-13009
chr12	83076551	83076950	E072	-12481
chr12	83089427	83089523	E072	0
chr12	83092107	83092306	E072	2676
chr12	83099426	83099466	E072	9995
chr12	83101396	83101633	E072	11965
chr12	83101788	83102841	E072	12357
chr12	83102895	83102978	E072	13464
chr12	83138139	83138299	E072	48708
chr12	83138485	83138589	E072	49054
chr12	83138687	83138737	E072	49256
chr12	83138749	83139207	E072	49318
chr12	83139300	83139355	E072	49869
chr12	83057758	83057933	E073	-31498
chr12	83057947	83058015	E073	-31416
chr12	83092107	83092306	E073	2676
chr12	83092649	83092732	E073	3218
chr12	83101788	83102841	E073	12357
chr12	83041757	83041835	E074	-47596
chr12	83044267	83045000	E074	-44431
chr12	83053447	83053645	E074	-35786
chr12	83053686	83053817	E074	-35614
chr12	83057758	83057933	E074	-31498
chr12	83058344	83058394	E074	-31037
chr12	83066965	83067196	E074	-22235
chr12	83075963	83076003	E074	-13428
chr12	83076067	83076422	E074	-13009
chr12	83076551	83076950	E074	-12481
chr12	83085844	83086057	E074	-3374
chr12	83086451	83086506	E074	-2925
chr12	83088814	83089100	E074	-331
chr12	83089427	83089523	E074	0
chr12	83089529	83089650	E074	98
chr12	83089703	83089759	E074	272
chr12	83092107	83092306	E074	2676
chr12	83092649	83092732	E074	3218
chr12	83092771	83092837	E074	3340
chr12	83099426	83099466	E074	9995
chr12	83099686	83099756	E074	10255
chr12	83099823	83099883	E074	10392
chr12	83100599	83100649	E074	11168
chr12	83100694	83100744	E074	11263
chr12	83100939	83101300	E074	11508
chr12	83101396	83101633	E074	11965
chr12	83101788	83102841	E074	12357
chr12	83102895	83102978	E074	13464
chr12	83103193	83103239	E074	13762
chr12	83103286	83103406	E074	13855
chr12	83103692	83104106	E074	14261
chr12	83124643	83125157	E074	35212
chr12	83125206	83125404	E074	35775
chr12	83125506	83125631	E074	36075
chr12	83138139	83138299	E074	48708
chr12	83138485	83138589	E074	49054
chr12	83138687	83138737	E074	49256
chr12	83138749	83139207	E074	49318
chr12	83139300	83139355	E074	49869
chr12	83075641	83075695	E081	-13736
chr12	83075963	83076003	E081	-13428
chr12	83076067	83076422	E081	-13009
chr12	83085844	83086057	E081	-3374
chr12	83076067	83076422	E082	-13009
chr12	83076551	83076950	E082	-12481
chr12	83085844	83086057	E082	-3374
chr12	83092771	83092837	E082	3340

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	83042094	83042312	E067	-47119
chr12	83079312	83082294	E067	-7137
chr12	83082295	83082382	E067	-7049
chr12	83082454	83082679	E067	-6752
chr12	83082690	83082846	E067	-6585
chr12	83083192	83083515	E067	-5916
chr12	83083636	83083923	E067	-5508
chr12	83083956	83084174	E067	-5257
chr12	83092881	83093376	E067	3450
chr12	83042094	83042312	E068	-47119
chr12	83079312	83082294	E068	-7137
chr12	83082295	83082382	E068	-7049
chr12	83082454	83082679	E068	-6752
chr12	83082690	83082846	E068	-6585
chr12	83083192	83083515	E068	-5916
chr12	83083636	83083923	E068	-5508
chr12	83083956	83084174	E068	-5257
chr12	83092881	83093376	E068	3450
chr12	83042094	83042312	E069	-47119
chr12	83079312	83082294	E069	-7137
chr12	83082295	83082382	E069	-7049
chr12	83082454	83082679	E069	-6752
chr12	83082690	83082846	E069	-6585
chr12	83083192	83083515	E069	-5916
chr12	83083636	83083923	E069	-5508
chr12	83083956	83084174	E069	-5257
chr12	83092881	83093376	E069	3450
chr12	83079312	83082294	E070	-7137
chr12	83082295	83082382	E070	-7049
chr12	83082454	83082679	E070	-6752
chr12	83082690	83082846	E070	-6585
chr12	83083192	83083515	E070	-5916
chr12	83083636	83083923	E070	-5508
chr12	83083956	83084174	E070	-5257
chr12	83092881	83093376	E070	3450
chr12	83042094	83042312	E071	-47119
chr12	83079312	83082294	E071	-7137
chr12	83082295	83082382	E071	-7049
chr12	83082454	83082679	E071	-6752
chr12	83082690	83082846	E071	-6585
chr12	83083192	83083515	E071	-5916
chr12	83083636	83083923	E071	-5508
chr12	83083956	83084174	E071	-5257
chr12	83092881	83093376	E071	3450
chr12	83042094	83042312	E072	-47119
chr12	83079312	83082294	E072	-7137
chr12	83082295	83082382	E072	-7049
chr12	83082454	83082679	E072	-6752
chr12	83082690	83082846	E072	-6585
chr12	83083192	83083515	E072	-5916
chr12	83083636	83083923	E072	-5508
chr12	83083956	83084174	E072	-5257
chr12	83092881	83093376	E072	3450
chr12	83079312	83082294	E073	-7137
chr12	83082295	83082382	E073	-7049
chr12	83082454	83082679	E073	-6752
chr12	83082690	83082846	E073	-6585
chr12	83083192	83083515	E073	-5916
chr12	83083636	83083923	E073	-5508
chr12	83083956	83084174	E073	-5257
chr12	83092881	83093376	E073	3450
chr12	83079312	83082294	E074	-7137
chr12	83082295	83082382	E074	-7049
chr12	83082454	83082679	E074	-6752
chr12	83082690	83082846	E074	-6585
chr12	83083192	83083515	E074	-5916
chr12	83083636	83083923	E074	-5508
chr12	83083956	83084174	E074	-5257
chr12	83092881	83093376	E074	3450
chr12	83079312	83082294	E081	-7137
chr12	83082295	83082382	E081	-7049
chr12	83082454	83082679	E081	-6752
chr12	83082690	83082846	E081	-6585
chr12	83079312	83082294	E082	-7137
chr12	83082295	83082382	E082	-7049
chr12	83082454	83082679	E082	-6752
chr12	83082690	83082846	E082	-6585
chr12	83083192	83083515	E082	-5916
chr12	83083636	83083923	E082	-5508
chr12	83083956	83084174	E082	-5257