rs13226386

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

HECW1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0455 (13634/29926,GnomAD)
G==0469 (13672/29118,TOPMED)
G==0493 (2470/5008,1000G)
G==0397 (1531/3854,ALSPAC)
G==0399 (1478/3708,TWINSUK)

Position: chr7:43528505 (GRCh38.p7) (7p13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 62 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.43528505G>A
GRCh38.p7 chr 7	NC_000007.14:g.43528505G>T
GRCh37.p13 chr 7	NC_000007.13:g.43568104G>A
GRCh37.p13 chr 7	NC_000007.13:g.43568104G>T

Gene: HECW1, HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HECW1 transcript variant 2	NM_001287059.1:c.	N/A	Intron Variant
HECW1 transcript variant 1	NM_015052.4:c.	N/A	Intron Variant
HECW1 transcript variant X6	XM_005249665.3:c.	N/A	Intron Variant
HECW1 transcript variant X4	XM_006715670.3:c.	N/A	Intron Variant
HECW1 transcript variant X5	XM_006715671.3:c.	N/A	Intron Variant
HECW1 transcript variant X15	XM_006715673.3:c.	N/A	Intron Variant
HECW1 transcript variant X8	XM_011515220.2:c.	N/A	Intron Variant
HECW1 transcript variant X12	XM_011515222.2:c.	N/A	Intron Variant
HECW1 transcript variant X13	XM_011515223.2:c.	N/A	Intron Variant
HECW1 transcript variant X14	XM_011515224.2:c.	N/A	Intron Variant
HECW1 transcript variant X17	XM_011515225.2:c.	N/A	Intron Variant
HECW1 transcript variant X18	XM_011515226.2:c.	N/A	Intron Variant
HECW1 transcript variant X1	XM_017011882.1:c.	N/A	Intron Variant
HECW1 transcript variant X2	XM_017011883.1:c.	N/A	Intron Variant
HECW1 transcript variant X3	XM_017011884.1:c.	N/A	Intron Variant
HECW1 transcript variant X7	XM_017011885.1:c.	N/A	Intron Variant
HECW1 transcript variant X9	XM_017011886.1:c.	N/A	Intron Variant
HECW1 transcript variant X10	XM_017011887.1:c.	N/A	Intron Variant
HECW1 transcript variant X11	XM_017011888.1:c.	N/A	Intron Variant
HECW1 transcript variant X16	XM_017011889.1:c.	N/A	Intron Variant
HECW1 transcript variant X19	XM_017011890.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.532	A=0.468
1000Genomes	American	Sub	694	G=0.470	A=0.530
1000Genomes	East Asian	Sub	1008	G=0.519	A=0.481
1000Genomes	Europe	Sub	1006	G=0.378	A=0.622
1000Genomes	Global	Study-wide	5008	G=0.493	A=0.507
1000Genomes	South Asian	Sub	978	G=0.550	A=0.450
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.397	A=0.603
The Genome Aggregation Database	African	Sub	8696	G=0.495	A=0.505
The Genome Aggregation Database	American	Sub	838	G=0.500	A=0.50,
The Genome Aggregation Database	East Asian	Sub	1610	G=0.499	A=0.501
The Genome Aggregation Database	Europe	Sub	18482	G=0.430	A=0.569
The Genome Aggregation Database	Global	Study-wide	29926	G=0.455	A=0.544
The Genome Aggregation Database	Other	Sub	300	G=0.510	A=0.49,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.469	A=0.530
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.399	A=0.601

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
rs13226386	0.000422	alcohol dependence	21314694

eQTL of rs13226386 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr7:43568104	COA1	ENSG00000106603.13	G>A	8.3608e-12	-201212	Cerebellum

meQTL of rs13226386 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 )
chr7	133811141	133811226	E067	-20257
chr7	133812985	133813062	E067	-18421
chr7	133825976	133826310	E067	-5173
chr7	133849497	133849547	E067	18014
chr7	133849627	133849694	E067	18144
chr7	133850044	133850308	E067	18561
chr7	133826381	133826535	E068	-4948
chr7	133849497	133849547	E068	18014
chr7	133849627	133849694	E068	18144
chr7	133850044	133850308	E068	18561
chr7	133849497	133849547	E069	18014
chr7	133849627	133849694	E069	18144
chr7	133850044	133850308	E069	18561
chr7	133814179	133814379	E070	-17104
chr7	133814428	133814612	E070	-16871
chr7	133815820	133815904	E070	-15579
chr7	133816172	133816256	E070	-15227
chr7	133816781	133816903	E070	-14580
chr7	133825698	133825955	E070	-5528
chr7	133825976	133826310	E070	-5173
chr7	133826381	133826535	E070	-4948
chr7	133826954	133827016	E070	-4467
chr7	133827149	133827199	E070	-4284
chr7	133827528	133827578	E070	-3905
chr7	133812985	133813062	E071	-18421
chr7	133849497	133849547	E071	18014
chr7	133849627	133849694	E071	18144
chr7	133850044	133850308	E071	18561
chr7	133851020	133851114	E071	19537
chr7	133812985	133813062	E072	-18421
chr7	133813090	133813210	E072	-18273
chr7	133849497	133849547	E072	18014
chr7	133849627	133849694	E072	18144
chr7	133850044	133850308	E072	18561
chr7	133812985	133813062	E074	-18421
chr7	133813090	133813210	E074	-18273
chr7	133849627	133849694	E074	18144
chr7	133850044	133850308	E074	18561
chr7	133851020	133851114	E074	19537
chr7	133810846	133810900	E081	-20583
chr7	133811141	133811226	E081	-20257
chr7	133812985	133813062	E081	-18421
chr7	133813090	133813210	E081	-18273
chr7	133862299	133862575	E081	30816
chr7	133862689	133862812	E081	31206
chr7	133863134	133863210	E081	31651
chr7	133863306	133863360	E081	31823
chr7	133863494	133864220	E081	32011
chr7	133864413	133864699	E081	32930
chr7	133878095	133878728	E081	46612
chr7	133878765	133878955	E081	47282
chr7	133811141	133811226	E082	-20257
chr7	133814627	133814717	E082	-16766
chr7	133815390	133815576	E082	-15907
chr7	133825698	133825955	E082	-5528
chr7	133825976	133826310	E082	-5173
chr7	133862299	133862575	E082	30816
chr7	133862689	133862812	E082	31206
chr7	133863134	133863210	E082	31651
chr7	133863306	133863360	E082	31823
chr7	133863494	133864220	E082	32011
chr7	133864413	133864699	E082	32930

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	133811532	133812695	E067	-18788
chr7	133812772	133812881	E067	-18602
chr7	133811532	133812695	E068	-18788
chr7	133812772	133812881	E068	-18602
chr7	133811532	133812695	E069	-18788
chr7	133812772	133812881	E069	-18602
chr7	133811532	133812695	E070	-18788
chr7	133812772	133812881	E070	-18602
chr7	133811532	133812695	E071	-18788
chr7	133811532	133812695	E072	-18788
chr7	133812772	133812881	E072	-18602
chr7	133811532	133812695	E073	-18788
chr7	133812772	133812881	E073	-18602
chr7	133811532	133812695	E074	-18788
chr7	133812772	133812881	E074	-18602
chr7	133811532	133812695	E081	-18788
chr7	133811532	133812695	E082	-18788
chr7	133812772	133812881	E082	-18602