rs11205760

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

FAF1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0307 (9199/29878,GnomAD)
T=0232 (6760/29118,TOPMED)
T=0368 (1843/5008,1000G)
T=0352 (1355/3854,ALSPAC)
T=0353 (1308/3708,TWINSUK)

Position: chr1:50708658 (GRCh38.p7) (1p32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 142 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.50708658C>T
GRCh37.p13 chr 1	NC_000001.10:g.51174330C>T

Gene: FAF1, Fas associated factor 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAF1 transcript	NM_007051.2:c.	N/A	Intron Variant
FAF1 transcript variant X3	XM_017000136.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.972	T=0.028
1000Genomes	American	Sub	694	C=0.470	T=0.530
1000Genomes	East Asian	Sub	1008	C=0.214	T=0.786
1000Genomes	Europe	Sub	1006	C=0.639	T=0.361
1000Genomes	Global	Study-wide	5008	C=0.632	T=0.368
1000Genomes	South Asian	Sub	978	C=0.710	T=0.290
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.648	T=0.352
The Genome Aggregation Database	African	Sub	8692	C=0.929	T=0.071
The Genome Aggregation Database	American	Sub	836	C=0.410	T=0.590
The Genome Aggregation Database	East Asian	Sub	1608	C=0.246	T=0.754
The Genome Aggregation Database	Europe	Sub	18440	C=0.630	T=0.369
The Genome Aggregation Database	Global	Study-wide	29878	C=0.692	T=0.307
The Genome Aggregation Database	Other	Sub	302	C=0.770	T=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.767	T=0.232
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.647	T=0.353

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
21295280	FAF1, a gene that is disrupted in cleft palate and has conserved function in zebrafish.	Ghassibe-Sabbagh M	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs11205760	0.0000337	alcoholism	pha002892
rs11205760	0.000034	alcohol dependence(early age of onset)	20201924
rs11205760	0.00069	alcohol dependence	20201924

eQTL of rs11205760 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 rs11205760 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	51125098	51125241	E067	-49089
chr1	51127372	51127746	E067	-46584
chr1	51131184	51131390	E067	-42940
chr1	51132638	51132812	E067	-41518
chr1	51133028	51133148	E067	-41182
chr1	51133203	51133317	E067	-41013
chr1	51133501	51133909	E067	-40421
chr1	51140964	51141041	E067	-33289
chr1	51165604	51166217	E067	-8113
chr1	51166227	51166313	E067	-8017
chr1	51167015	51167105	E067	-7225
chr1	51167506	51167629	E067	-6701
chr1	51167776	51167877	E067	-6453
chr1	51170785	51170829	E067	-3501
chr1	51170979	51171040	E067	-3290
chr1	51171427	51171773	E067	-2557
chr1	51171906	51171970	E067	-2360
chr1	51214961	51215166	E067	40631
chr1	51125098	51125241	E068	-49089
chr1	51127372	51127746	E068	-46584
chr1	51131184	51131390	E068	-42940
chr1	51132638	51132812	E068	-41518
chr1	51133028	51133148	E068	-41182
chr1	51133203	51133317	E068	-41013
chr1	51133501	51133909	E068	-40421
chr1	51165604	51166217	E068	-8113
chr1	51166227	51166313	E068	-8017
chr1	51167015	51167105	E068	-7225
chr1	51169030	51169118	E068	-5212
chr1	51170785	51170829	E068	-3501
chr1	51170979	51171040	E068	-3290
chr1	51171427	51171773	E068	-2557
chr1	51214961	51215166	E068	40631
chr1	51125098	51125241	E069	-49089
chr1	51127372	51127746	E069	-46584
chr1	51131184	51131390	E069	-42940
chr1	51132638	51132812	E069	-41518
chr1	51133028	51133148	E069	-41182
chr1	51133203	51133317	E069	-41013
chr1	51133501	51133909	E069	-40421
chr1	51134819	51134891	E069	-39439
chr1	51140964	51141041	E069	-33289
chr1	51149956	51150197	E069	-24133
chr1	51163078	51164014	E069	-10316
chr1	51164051	51164131	E069	-10199
chr1	51165604	51166217	E069	-8113
chr1	51166227	51166313	E069	-8017
chr1	51167015	51167105	E069	-7225
chr1	51167506	51167629	E069	-6701
chr1	51167776	51167877	E069	-6453
chr1	51168559	51168603	E069	-5727
chr1	51169030	51169118	E069	-5212
chr1	51170785	51170829	E069	-3501
chr1	51170979	51171040	E069	-3290
chr1	51171427	51171773	E069	-2557
chr1	51183438	51183478	E069	9108
chr1	51214961	51215166	E069	40631
chr1	51133028	51133148	E070	-41182
chr1	51133203	51133317	E070	-41013
chr1	51133501	51133909	E070	-40421
chr1	51140964	51141041	E070	-33289
chr1	51165604	51166217	E070	-8113
chr1	51125098	51125241	E071	-49089
chr1	51127372	51127746	E071	-46584
chr1	51131184	51131390	E071	-42940
chr1	51132638	51132812	E071	-41518
chr1	51133028	51133148	E071	-41182
chr1	51133203	51133317	E071	-41013
chr1	51133501	51133909	E071	-40421
chr1	51140964	51141041	E071	-33289
chr1	51149956	51150197	E071	-24133
chr1	51163078	51164014	E071	-10316
chr1	51164051	51164131	E071	-10199
chr1	51166227	51166313	E071	-8017
chr1	51167015	51167105	E071	-7225
chr1	51168559	51168603	E071	-5727
chr1	51169030	51169118	E071	-5212
chr1	51170785	51170829	E071	-3501
chr1	51170979	51171040	E071	-3290
chr1	51171427	51171773	E071	-2557
chr1	51171906	51171970	E071	-2360
chr1	51183068	51183352	E071	8738
chr1	51183438	51183478	E071	9108
chr1	51199276	51199381	E071	24946
chr1	51214961	51215166	E071	40631
chr1	51125098	51125241	E072	-49089
chr1	51132638	51132812	E072	-41518
chr1	51133028	51133148	E072	-41182
chr1	51133203	51133317	E072	-41013
chr1	51133501	51133909	E072	-40421
chr1	51140964	51141041	E072	-33289
chr1	51163078	51164014	E072	-10316
chr1	51164051	51164131	E072	-10199
chr1	51165604	51166217	E072	-8113
chr1	51166227	51166313	E072	-8017
chr1	51167015	51167105	E072	-7225
chr1	51167506	51167629	E072	-6701
chr1	51167776	51167877	E072	-6453
chr1	51168559	51168603	E072	-5727
chr1	51169030	51169118	E072	-5212
chr1	51170785	51170829	E072	-3501
chr1	51170979	51171040	E072	-3290
chr1	51171427	51171773	E072	-2557
chr1	51171906	51171970	E072	-2360
chr1	51183068	51183352	E072	8738
chr1	51183438	51183478	E072	9108
chr1	51184697	51184826	E072	10367
chr1	51184899	51185064	E072	10569
chr1	51214961	51215166	E072	40631
chr1	51127372	51127746	E073	-46584
chr1	51131184	51131390	E073	-42940
chr1	51140964	51141041	E073	-33289
chr1	51169030	51169118	E073	-5212
chr1	51125098	51125241	E074	-49089
chr1	51127372	51127746	E074	-46584
chr1	51132638	51132812	E074	-41518
chr1	51133028	51133148	E074	-41182
chr1	51133203	51133317	E074	-41013
chr1	51133501	51133909	E074	-40421
chr1	51140964	51141041	E074	-33289
chr1	51149956	51150197	E074	-24133
chr1	51163078	51164014	E074	-10316
chr1	51164051	51164131	E074	-10199
chr1	51165604	51166217	E074	-8113
chr1	51166227	51166313	E074	-8017
chr1	51167015	51167105	E074	-7225
chr1	51167506	51167629	E074	-6701
chr1	51167776	51167877	E074	-6453
chr1	51168559	51168603	E074	-5727
chr1	51169030	51169118	E074	-5212
chr1	51169817	51169995	E074	-4335
chr1	51170785	51170829	E074	-3501
chr1	51170979	51171040	E074	-3290
chr1	51171427	51171773	E074	-2557
chr1	51183068	51183352	E074	8738
chr1	51184697	51184826	E074	10367
chr1	51184899	51185064	E074	10569
chr1	51199276	51199381	E074	24946
chr1	51214961	51215166	E074	40631
chr1	51165604	51166217	E082	-8113
chr1	51167506	51167629	E082	-6701
chr1	51167776	51167877	E082	-6453