rs12135256

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

ASTN1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0435 (12966/29794,GnomAD)
C==0441 (12841/29118,TOPMED)
G=0456 (2282/5008,1000G)
C==0412 (1586/3854,ALSPAC)
C==0402 (1491/3708,TWINSUK)

Position: chr1:177006309 (GRCh38.p7) (1q25.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 91 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.177006309C>G
GRCh37.p13 chr 1	NC_000001.10:g.176975445C>G

Gene: ASTN1, astrotactin 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ASTN1 transcript variant 3	NM_001286164.1:c.	N/A	Intron Variant
ASTN1 transcript variant 1	NM_004319.2:c.	N/A	Intron Variant
ASTN1 transcript variant 2	NM_207108.2:c.	N/A	Intron Variant
ASTN1 transcript variant X1	XM_017001340.1:c.	N/A	Intron Variant
ASTN1 transcript variant X2	XM_017001341.1:c.	N/A	Intron Variant
ASTN1 transcript variant X3	XR_001737193.1:n.	N/A	Intron Variant
ASTN1 transcript variant X4	XR_001737194.1:n.	N/A	Intron Variant
ASTN1 transcript variant X5	XR_921796.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.386	G=0.614
1000Genomes	American	Sub	694	C=0.530	G=0.470
1000Genomes	East Asian	Sub	1008	C=0.803	G=0.197
1000Genomes	Europe	Sub	1006	C=0.437	G=0.563
1000Genomes	Global	Study-wide	5008	C=0.544	G=0.456
1000Genomes	South Asian	Sub	978	C=0.610	G=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.412	G=0.588
The Genome Aggregation Database	African	Sub	8682	C=0.407	G=0.593
The Genome Aggregation Database	American	Sub	828	C=0.570	G=0.430
The Genome Aggregation Database	East Asian	Sub	1614	C=0.814	G=0.186
The Genome Aggregation Database	Europe	Sub	18370	C=0.409	G=0.590
The Genome Aggregation Database	Global	Study-wide	29794	C=0.435	G=0.564
The Genome Aggregation Database	Other	Sub	300	C=0.410	G=0.590
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.441	G=0.559
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.402	G=0.598

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12135256	0.000976	alcohol dependence	21314694

eQTL of rs12135256 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 rs12135256 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	176927955	176928206	E067	-47239
chr1	176928354	176928619	E067	-46826
chr1	176928683	176928852	E067	-46593
chr1	176929111	176929169	E067	-46276
chr1	177003346	177003518	E067	27901
chr1	177003870	177003965	E067	28425
chr1	177004113	177004279	E067	28668
chr1	176927955	176928206	E068	-47239
chr1	176928354	176928619	E068	-46826
chr1	176928683	176928852	E068	-46593
chr1	176958218	176958715	E068	-16730
chr1	176965551	176966063	E068	-9382
chr1	176968437	176968562	E068	-6883
chr1	176993893	176993960	E068	18448
chr1	176994199	176994274	E068	18754
chr1	177003346	177003518	E068	27901
chr1	177017922	177018090	E068	42477
chr1	177019276	177019320	E068	43831
chr1	177019415	177019773	E068	43970
chr1	176927955	176928206	E069	-47239
chr1	176928354	176928619	E069	-46826
chr1	176928683	176928852	E069	-46593
chr1	176929111	176929169	E069	-46276
chr1	176976833	176976931	E069	1388
chr1	176992649	176992704	E069	17204
chr1	176992974	176993199	E069	17529
chr1	176993893	176993960	E069	18448
chr1	176994199	176994274	E069	18754
chr1	177003346	177003518	E069	27901
chr1	177003870	177003965	E069	28425
chr1	177004873	177004997	E069	29428
chr1	176926745	176927001	E070	-48444
chr1	176929111	176929169	E070	-46276
chr1	176936692	176936869	E070	-38576
chr1	176953028	176953138	E070	-22307
chr1	176992974	176993199	E070	17529
chr1	176993893	176993960	E070	18448
chr1	176994199	176994274	E070	18754
chr1	177013188	177013270	E070	37743
chr1	177013496	177013932	E070	38051
chr1	176965237	176965547	E071	-9898
chr1	176965551	176966063	E071	-9382
chr1	176992974	176993199	E071	17529
chr1	176952931	176953016	E072	-22429
chr1	176953028	176953138	E072	-22307
chr1	176993893	176993960	E072	18448
chr1	177002781	177003086	E072	27336
chr1	177003346	177003518	E072	27901
chr1	177003870	177003965	E072	28425
chr1	177004873	177004997	E072	29428
chr1	176927955	176928206	E073	-47239
chr1	176928354	176928619	E073	-46826
chr1	176928683	176928852	E073	-46593
chr1	176929111	176929169	E073	-46276
chr1	176952931	176953016	E073	-22429
chr1	176953028	176953138	E073	-22307
chr1	176976833	176976931	E073	1388
chr1	176977013	176977265	E073	1568
chr1	176983459	176983993	E073	8014
chr1	176992974	176993199	E073	17529
chr1	177004113	177004279	E073	28668
chr1	177017922	177018090	E073	42477
chr1	176992649	176992704	E074	17204
chr1	176992974	176993199	E074	17529
chr1	176927955	176928206	E081	-47239
chr1	176928354	176928619	E081	-46826
chr1	176928683	176928852	E081	-46593
chr1	176933807	176934123	E081	-41322
chr1	176934497	176934550	E081	-40895
chr1	176945481	176945706	E081	-29739
chr1	176986225	176987011	E081	10780
chr1	176989407	176989624	E081	13962
chr1	176989771	176990576	E081	14326
chr1	176990614	176990809	E081	15169
chr1	176990846	176991203	E081	15401
chr1	176992649	176992704	E081	17204
chr1	176992974	176993199	E081	17529
chr1	176993893	176993960	E081	18448
chr1	176994199	176994274	E081	18754
chr1	176927955	176928206	E082	-47239
chr1	176928354	176928619	E082	-46826
chr1	176928683	176928852	E082	-46593
chr1	176929111	176929169	E082	-46276
chr1	176933807	176934123	E082	-41322
chr1	176936692	176936869	E082	-38576
chr1	176953962	176954144	E082	-21301
chr1	176958947	176959357	E082	-16088
chr1	176992974	176993199	E082	17529
chr1	176993893	176993960	E082	18448
chr1	176994199	176994274	E082	18754
chr1	177012887	177012978	E082	37442