rs612414

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0287 (8602/29912,GnomAD)
T=0230 (1154/5008,1000G)
T=0370 (1425/3854,ALSPAC)
T=0378 (1403/3708,TWINSUK)

Position: chr1:212428834 (GRCh38.p7) (1q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 85 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.212428834G>A
GRCh38.p7 chr 1	NC_000001.11:g.212428834G>T
GRCh37.p13 chr 1	NC_000001.10:g.212602176G>A
GRCh37.p13 chr 1	NC_000001.10:g.212602176G>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.771	T=0.229
1000Genomes	American	Sub	694	G=0.730	T=0.270
1000Genomes	East Asian	Sub	1008	G=0.880	T=0.120
1000Genomes	Europe	Sub	1006	G=0.622	T=0.378
1000Genomes	Global	Study-wide	5008	G=0.770	T=0.230
1000Genomes	South Asian	Sub	978	G=0.840	T=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.630	T=0.370
The Genome Aggregation Database	African	Sub	8714	G=0.738	A=0.000
The Genome Aggregation Database	American	Sub	828	G=0.710	A=0.00,
The Genome Aggregation Database	East Asian	Sub	1616	G=0.881	A=0.000
The Genome Aggregation Database	Europe	Sub	18452	G=0.686	A=0.000
The Genome Aggregation Database	Global	Study-wide	29912	G=0.712	A=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.640	A=0.00,
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.622	T=0.378

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
rs612414	1.0661E-05	alcohol dependence	23089632

eQTL of rs612414 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:212602176	TMEM206	ENSG00000065600.8	G>T	8.4147e-6	13933	Caudate_basal_ganglia
Chr1:212602176	TMEM206	ENSG00000065600.8	G>T	8.5460e-6	13933	Brain_Spinal_cord_cervical
Chr1:212602176	TMEM206	ENSG00000065600.8	G>T	2.9890e-5	13933	Hippocampus
Chr1:212602176	TMEM206	ENSG00000065600.8	G>T	6.7478e-4	13933	Putamen_basal_ganglia

meQTL of rs612414 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 )
chr1	6830752	6830833	E067	14804
chr1	6830837	6831378	E067	14889
chr1	6847509	6847606	E067	31561
chr1	6847660	6847700	E067	31712
chr1	6847957	6848020	E067	32009
chr1	6849162	6849363	E067	33214
chr1	6849463	6849809	E067	33515
chr1	6850310	6850389	E067	34362
chr1	6862075	6862479	E067	46127
chr1	6862623	6862673	E067	46675
chr1	6862691	6862763	E067	46743
chr1	6794953	6795157	E068	-20791
chr1	6795210	6795440	E068	-20508
chr1	6795623	6795694	E068	-20254
chr1	6795813	6795949	E068	-19999
chr1	6849463	6849809	E068	33515
chr1	6850310	6850389	E068	34362
chr1	6851383	6851433	E068	35435
chr1	6794953	6795157	E069	-20791
chr1	6795210	6795440	E069	-20508
chr1	6795623	6795694	E069	-20254
chr1	6795813	6795949	E069	-19999
chr1	6843469	6843552	E069	27521
chr1	6847509	6847606	E069	31561
chr1	6847660	6847700	E069	31712
chr1	6849463	6849809	E069	33515
chr1	6850310	6850389	E069	34362
chr1	6855751	6856107	E069	39803
chr1	6862623	6862673	E069	46675
chr1	6862691	6862763	E069	46743
chr1	6865213	6865403	E069	49265
chr1	6865406	6865459	E069	49458
chr1	6832144	6832282	E070	16196
chr1	6847509	6847606	E070	31561
chr1	6847660	6847700	E070	31712
chr1	6847957	6848020	E070	32009
chr1	6861181	6861267	E070	45233
chr1	6861317	6861512	E070	45369
chr1	6865102	6865183	E070	49154
chr1	6865213	6865403	E070	49265
chr1	6865406	6865459	E070	49458
chr1	6794953	6795157	E071	-20791
chr1	6795210	6795440	E071	-20508
chr1	6795623	6795694	E071	-20254
chr1	6795813	6795949	E071	-19999
chr1	6803178	6804238	E071	-11710
chr1	6843469	6843552	E071	27521
chr1	6847509	6847606	E071	31561
chr1	6847660	6847700	E071	31712
chr1	6847957	6848020	E071	32009
chr1	6848252	6848348	E071	32304
chr1	6849162	6849363	E071	33214
chr1	6855751	6856107	E071	39803
chr1	6856235	6856318	E071	40287
chr1	6856742	6856908	E071	40794
chr1	6861317	6861512	E071	45369
chr1	6862075	6862479	E071	46127
chr1	6862623	6862673	E071	46675
chr1	6862691	6862763	E071	46743
chr1	6865102	6865183	E071	49154
chr1	6865213	6865403	E071	49265
chr1	6865406	6865459	E071	49458
chr1	6795210	6795440	E072	-20508
chr1	6795623	6795694	E072	-20254
chr1	6795813	6795949	E072	-19999
chr1	6847509	6847606	E072	31561
chr1	6847660	6847700	E072	31712
chr1	6849162	6849363	E072	33214
chr1	6843469	6843552	E073	27521
chr1	6847509	6847606	E073	31561
chr1	6847660	6847700	E073	31712
chr1	6849162	6849363	E073	33214
chr1	6861181	6861267	E073	45233
chr1	6861317	6861512	E073	45369
chr1	6795210	6795440	E074	-20508
chr1	6849162	6849363	E074	33214
chr1	6849463	6849809	E074	33515
chr1	6856742	6856908	E074	40794
chr1	6862075	6862479	E074	46127
chr1	6862623	6862673	E074	46675
chr1	6862691	6862763	E074	46743
chr1	6865102	6865183	E074	49154
chr1	6865213	6865403	E074	49265
chr1	6865406	6865459	E074	49458
chr1	6849162	6849363	E082	33214

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	6843876	6846731	E067	27928
chr1	6843876	6846731	E068	27928
chr1	6843876	6846731	E069	27928
chr1	6843876	6846731	E070	27928
chr1	6843876	6846731	E071	27928
chr1	6843876	6846731	E072	27928
chr1	6843876	6846731	E073	27928
chr1	6843876	6846731	E074	27928
chr1	6843876	6846731	E082	27928