rs506879

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0290 (8678/29912,GnomAD)
A=0315 (9177/29118,TOPMED)
A=0320 (1601/5008,1000G)
A=0247 (952/3854,ALSPAC)
A=0235 (872/3708,TWINSUK)

Position: chr6:165167517 (GRCh38.p7) (6q27)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 100 Enhancers around

Promoter: 87 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.165167517C>A
GRCh38.p7 chr 6	NC_000006.12:g.165167517C>T
GRCh37.p13 chr 6	NC_000006.11:g.165581006C>A
GRCh37.p13 chr 6	NC_000006.11:g.165581006C>T

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.596	A=0.404
1000Genomes	American	Sub	694	C=0.680	A=0.320
1000Genomes	East Asian	Sub	1008	C=0.692	A=0.308
1000Genomes	Europe	Sub	1006	C=0.764	A=0.236
1000Genomes	Global	Study-wide	5008	C=0.680	A=0.320
1000Genomes	South Asian	Sub	978	C=0.700	A=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.753	A=0.247
The Genome Aggregation Database	African	Sub	8710	C=0.607	A=0.393
The Genome Aggregation Database	American	Sub	836	C=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1612	C=0.743	A=0.257
The Genome Aggregation Database	Europe	Sub	18454	C=0.756	A=0.243
The Genome Aggregation Database	Global	Study-wide	29912	C=0.709	A=0.290
The Genome Aggregation Database	Other	Sub	300	C=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.684	A=0.315
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.765	A=0.235

PMID	Title	Author	Journal
27151647	An association study revealed substantial effects of dominance, epistasis and substance dependence co-morbidity on alcohol dependence symptom count.	Chen G	Addict Biol

SNP ID	p-value	Traits	Study
rs506879	8E-07	alcohol dependence	27151647

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr6	30613764	30613855	E067	-42992
chr6	30613862	30613940	E067	-42907
chr6	30638362	30638412	E067	-18435
chr6	30638663	30638784	E067	-18063
chr6	30647331	30647646	E067	-9201
chr6	30647723	30648016	E067	-8831
chr6	30648040	30648227	E067	-8620
chr6	30648246	30648343	E067	-8504
chr6	30686594	30686665	E067	29747
chr6	30686701	30686781	E067	29854
chr6	30613648	30613754	E068	-43093
chr6	30613764	30613855	E068	-42992
chr6	30613862	30613940	E068	-42907
chr6	30638925	30639043	E068	-17804
chr6	30647723	30648016	E068	-8831
chr6	30648040	30648227	E068	-8620
chr6	30648246	30648343	E068	-8504
chr6	30686480	30686536	E068	29633
chr6	30686594	30686665	E068	29747
chr6	30686701	30686781	E068	29854
chr6	30690777	30690978	E068	33930
chr6	30613764	30613855	E069	-42992
chr6	30613862	30613940	E069	-42907
chr6	30614002	30614069	E069	-42778
chr6	30638663	30638784	E069	-18063
chr6	30638925	30639043	E069	-17804
chr6	30646637	30647246	E069	-9601
chr6	30647331	30647646	E069	-9201
chr6	30686480	30686536	E069	29633
chr6	30686594	30686665	E069	29747
chr6	30686701	30686781	E069	29854
chr6	30690777	30690978	E069	33930
chr6	30703881	30704025	E069	47034
chr6	30704151	30704194	E069	47304
chr6	30613648	30613754	E070	-43093
chr6	30613764	30613855	E070	-42992
chr6	30613862	30613940	E070	-42907
chr6	30614002	30614069	E070	-42778
chr6	30638663	30638784	E070	-18063
chr6	30638925	30639043	E070	-17804
chr6	30646637	30647246	E070	-9601
chr6	30647331	30647646	E070	-9201
chr6	30613764	30613855	E071	-42992
chr6	30613862	30613940	E071	-42907
chr6	30638925	30639043	E071	-17804
chr6	30656353	30656751	E071	-96
chr6	30647723	30648016	E072	-8831
chr6	30648040	30648227	E072	-8620
chr6	30648246	30648343	E072	-8504
chr6	30638925	30639043	E073	-17804
chr6	30646637	30647246	E073	-9601
chr6	30647723	30648016	E073	-8831
chr6	30690777	30690978	E073	33930
chr6	30698004	30698048	E073	41157
chr6	30698095	30698145	E073	41248
chr6	30698168	30698276	E073	41321
chr6	30698462	30698970	E073	41615
chr6	30705947	30706007	E073	49100
chr6	30706086	30706193	E073	49239
chr6	30613862	30613940	E074	-42907
chr6	30614002	30614069	E074	-42778
chr6	30647331	30647646	E074	-9201
chr6	30647723	30648016	E074	-8831
chr6	30686480	30686536	E074	29633
chr6	30686594	30686665	E074	29747
chr6	30686701	30686781	E074	29854
chr6	30690777	30690978	E074	33930
chr6	30613648	30613754	E081	-43093
chr6	30613764	30613855	E081	-42992
chr6	30613862	30613940	E081	-42907
chr6	30614002	30614069	E081	-42778
chr6	30646637	30647246	E081	-9601
chr6	30647331	30647646	E081	-9201
chr6	30647723	30648016	E081	-8831
chr6	30648040	30648227	E081	-8620
chr6	30648246	30648343	E081	-8504
chr6	30656353	30656751	E081	-96
chr6	30656850	30657058	E081	3
chr6	30657178	30657279	E081	331
chr6	30686480	30686536	E081	29633
chr6	30686594	30686665	E081	29747
chr6	30686701	30686781	E081	29854
chr6	30691023	30691114	E081	34176
chr6	30691348	30691798	E081	34501
chr6	30691856	30692001	E081	35009
chr6	30692129	30692212	E081	35282
chr6	30692398	30692503	E081	35551
chr6	30692707	30692787	E081	35860
chr6	30692818	30692911	E081	35971
chr6	30692946	30693241	E081	36099
chr6	30693463	30694162	E081	36616
chr6	30617345	30617395	E082	-39452
chr6	30638362	30638412	E082	-18435
chr6	30638663	30638784	E082	-18063
chr6	30638925	30639043	E082	-17804
chr6	30656850	30657058	E082	3
chr6	30657178	30657279	E082	331
chr6	30686480	30686536	E082	29633
chr6	30686594	30686665	E082	29747
chr6	30686701	30686781	E082	29854

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	30614199	30616235	E067	-40612
chr6	30640128	30641215	E067	-15632
chr6	30649587	30651702	E067	-5145
chr6	30651763	30652041	E067	-4806
chr6	30652110	30652236	E067	-4611
chr6	30652241	30652947	E067	-3900
chr6	30652981	30656320	E067	-527
chr6	30684628	30685787	E067	27781
chr6	30687090	30689981	E067	30243
chr6	30690025	30690105	E067	33178
chr6	30614199	30616235	E068	-40612
chr6	30640128	30641215	E068	-15632
chr6	30649587	30651702	E068	-5145
chr6	30651763	30652041	E068	-4806
chr6	30652110	30652236	E068	-4611
chr6	30652241	30652947	E068	-3900
chr6	30652981	30656320	E068	-527
chr6	30684628	30685787	E068	27781
chr6	30687090	30689981	E068	30243
chr6	30690025	30690105	E068	33178
chr6	30614199	30616235	E069	-40612
chr6	30640128	30641215	E069	-15632
chr6	30649587	30651702	E069	-5145
chr6	30651763	30652041	E069	-4806
chr6	30652110	30652236	E069	-4611
chr6	30652241	30652947	E069	-3900
chr6	30652981	30656320	E069	-527
chr6	30684628	30685787	E069	27781
chr6	30687090	30689981	E069	30243
chr6	30614199	30616235	E070	-40612
chr6	30640128	30641215	E070	-15632
chr6	30649587	30651702	E070	-5145
chr6	30652981	30656320	E070	-527
chr6	30684628	30685787	E070	27781
chr6	30687090	30689981	E070	30243
chr6	30614199	30616235	E071	-40612
chr6	30640128	30641215	E071	-15632
chr6	30649587	30651702	E071	-5145
chr6	30651763	30652041	E071	-4806
chr6	30652110	30652236	E071	-4611
chr6	30652241	30652947	E071	-3900
chr6	30652981	30656320	E071	-527
chr6	30684628	30685787	E071	27781
chr6	30687090	30689981	E071	30243
chr6	30690025	30690105	E071	33178
chr6	30614199	30616235	E072	-40612
chr6	30640128	30641215	E072	-15632
chr6	30649587	30651702	E072	-5145
chr6	30651763	30652041	E072	-4806
chr6	30652110	30652236	E072	-4611
chr6	30652241	30652947	E072	-3900
chr6	30652981	30656320	E072	-527
chr6	30684628	30685787	E072	27781
chr6	30687090	30689981	E072	30243
chr6	30690025	30690105	E072	33178
chr6	30614199	30616235	E073	-40612
chr6	30640128	30641215	E073	-15632
chr6	30649587	30651702	E073	-5145
chr6	30651763	30652041	E073	-4806
chr6	30652110	30652236	E073	-4611
chr6	30652241	30652947	E073	-3900
chr6	30652981	30656320	E073	-527
chr6	30684628	30685787	E073	27781
chr6	30687090	30689981	E073	30243
chr6	30690025	30690105	E073	33178
chr6	30614199	30616235	E074	-40612
chr6	30640128	30641215	E074	-15632
chr6	30649587	30651702	E074	-5145
chr6	30651763	30652041	E074	-4806
chr6	30652110	30652236	E074	-4611
chr6	30652241	30652947	E074	-3900
chr6	30652981	30656320	E074	-527
chr6	30684628	30685787	E074	27781
chr6	30687090	30689981	E074	30243
chr6	30690025	30690105	E074	33178
chr6	30640128	30641215	E081	-15632
chr6	30651763	30652041	E081	-4806
chr6	30652110	30652236	E081	-4611
chr6	30684628	30685787	E081	27781
chr6	30687090	30689981	E081	30243
chr6	30690025	30690105	E081	33178
chr6	30614199	30616235	E082	-40612
chr6	30640128	30641215	E082	-15632
chr6	30652981	30656320	E082	-527
chr6	30684628	30685787	E082	27781
chr6	30687090	30689981	E082	30243
chr6	30690025	30690105	E082	33178

rs506879

Genomic Coordinates

Population Frequency

P-Value

eQTL of rs506879 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs506879 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)