rs61908460

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CCDC77 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0163 (4910/29952,GnomAD)
T=0118 (3439/29118,TOPMED)
T=0118 (593/5008,1000G)
T=0203 (784/3854,ALSPAC)
T=0202 (748/3708,TWINSUK)

Position: chr12:414895 (GRCh38.p7) (12p13.33)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 35 Enhancers around

Promoter: 71 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.414895C>T
GRCh37.p13 chr 12	NC_000012.11:g.524061C>T

Gene: CCDC77, coiled-coil domain containing 77(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCDC77 transcript variant 2	NM_001130146.1:c.	N/A	Intron Variant
CCDC77 transcript variant 3	NM_001130147.1:c.	N/A	Intron Variant
CCDC77 transcript variant 4	NM_001130148.1:c.	N/A	Intron Variant
CCDC77 transcript variant 1	NM_032358.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.992	T=0.008
1000Genomes	American	Sub	694	C=0.880	T=0.120
1000Genomes	East Asian	Sub	1008	C=0.925	T=0.075
1000Genomes	Europe	Sub	1006	C=0.806	T=0.194
1000Genomes	Global	Study-wide	5008	C=0.882	T=0.118
1000Genomes	South Asian	Sub	978	C=0.770	T=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.797	T=0.203
The Genome Aggregation Database	African	Sub	8724	C=0.964	T=0.036
The Genome Aggregation Database	American	Sub	836	C=0.870	T=0.130
The Genome Aggregation Database	East Asian	Sub	1618	C=0.892	T=0.108
The Genome Aggregation Database	Europe	Sub	18472	C=0.769	T=0.230
The Genome Aggregation Database	Global	Study-wide	29952	C=0.836	T=0.163
The Genome Aggregation Database	Other	Sub	302	C=0.820	T=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.881	T=0.118
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.798	T=0.202

PMID	Title	Author	Journal
29460428	Genomewide Association Study of Alcohol Dependence and Related Traits in a Thai Population.	Gelernter J	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs61908460	7E-06	alcohol consumption measurement	29460428

eQTL of rs61908460 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 rs61908460 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	494899	495143	E067	-28918
chr12	495224	495274	E067	-28787
chr12	495555	495666	E067	-28395
chr12	551383	551778	E067	27322
chr12	495555	495666	E068	-28395
chr12	531437	531552	E068	7376
chr12	494899	495143	E069	-28918
chr12	495224	495274	E069	-28787
chr12	495555	495666	E069	-28395
chr12	494899	495143	E070	-28918
chr12	512338	512388	E070	-11673
chr12	523775	523927	E070	-134
chr12	523969	524067	E070	0
chr12	524190	524378	E070	129
chr12	559474	559680	E070	35413
chr12	495555	495666	E071	-28395
chr12	516035	516379	E071	-7682
chr12	516501	516541	E071	-7520
chr12	516648	516773	E071	-7288
chr12	494899	495143	E072	-28918
chr12	495224	495274	E072	-28787
chr12	495555	495666	E072	-28395
chr12	495555	495666	E073	-28395
chr12	494899	495143	E074	-28918
chr12	495224	495274	E074	-28787
chr12	495555	495666	E074	-28395
chr12	494899	495143	E081	-28918
chr12	495224	495274	E081	-28787
chr12	495555	495666	E081	-28395
chr12	512002	512126	E081	-11935
chr12	512338	512388	E081	-11673
chr12	568205	568269	E081	44144
chr12	523775	523927	E082	-134
chr12	523969	524067	E082	0
chr12	524190	524378	E082	129

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	496747	496892	E067	-27169
chr12	496946	497403	E067	-26658
chr12	497456	499261	E067	-24800
chr12	510088	511708	E067	-12353
chr12	568364	569471	E067	44303
chr12	569495	569973	E067	45434
chr12	496747	496892	E068	-27169
chr12	496946	497403	E068	-26658
chr12	497456	499261	E068	-24800
chr12	510088	511708	E068	-12353
chr12	562552	563252	E068	38491
chr12	568364	569471	E068	44303
chr12	569495	569973	E068	45434
chr12	570050	570451	E068	45989
chr12	496747	496892	E069	-27169
chr12	496946	497403	E069	-26658
chr12	497456	499261	E069	-24800
chr12	510088	511708	E069	-12353
chr12	568364	569471	E069	44303
chr12	569495	569973	E069	45434
chr12	570050	570451	E069	45989
chr12	496747	496892	E070	-27169
chr12	496946	497403	E070	-26658
chr12	497456	499261	E070	-24800
chr12	510088	511708	E070	-12353
chr12	568364	569471	E070	44303
chr12	569495	569973	E070	45434
chr12	570050	570451	E070	45989
chr12	496747	496892	E071	-27169
chr12	496946	497403	E071	-26658
chr12	497456	499261	E071	-24800
chr12	510088	511708	E071	-12353
chr12	562552	563252	E071	38491
chr12	568364	569471	E071	44303
chr12	569495	569973	E071	45434
chr12	570050	570451	E071	45989
chr12	570494	570579	E071	46433
chr12	496747	496892	E072	-27169
chr12	496946	497403	E072	-26658
chr12	497456	499261	E072	-24800
chr12	510088	511708	E072	-12353
chr12	562552	563252	E072	38491
chr12	568364	569471	E072	44303
chr12	569495	569973	E072	45434
chr12	570050	570451	E072	45989
chr12	570494	570579	E072	46433
chr12	496747	496892	E073	-27169
chr12	496946	497403	E073	-26658
chr12	497456	499261	E073	-24800
chr12	510088	511708	E073	-12353
chr12	568364	569471	E073	44303
chr12	569495	569973	E073	45434
chr12	570050	570451	E073	45989
chr12	570494	570579	E073	46433
chr12	496747	496892	E074	-27169
chr12	496946	497403	E074	-26658
chr12	497456	499261	E074	-24800
chr12	510088	511708	E074	-12353
chr12	562552	563252	E074	38491
chr12	496747	496892	E081	-27169
chr12	496946	497403	E081	-26658
chr12	497456	499261	E081	-24800
chr12	510088	511708	E081	-12353
chr12	496747	496892	E082	-27169
chr12	496946	497403	E082	-26658
chr12	497456	499261	E082	-24800
chr12	510088	511708	E082	-12353
chr12	568364	569471	E082	44303
chr12	569495	569973	E082	45434
chr12	570050	570451	E082	45989
chr12	570494	570579	E082	46433