rs2513929

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC101927245 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0237 (7114/29956,GnomAD)
T=0226 (6604/29118,TOPMED)
T=0288 (1442/5008,1000G)
T=0223 (859/3854,ALSPAC)
T=0220 (817/3708,TWINSUK)

Position: chr8:102702118 (GRCh38.p7) (8q22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 36 Enhancers around

Promoter: 9 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.102702118C>T
GRCh37.p13 chr 8	NC_000008.10:g.103714346C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101927245 transcript variant X1	XM_011517419.2:c.	N/A	Genic Downstream Transcript Variant
LOC101927245 transcript variant X3	XM_011517420.2:c.	N/A	Genic Downstream Transcript Variant
LOC101927245 transcript variant X9	XR_001746024.1:n.	N/A	Intron Variant
LOC101927245 transcript variant X11	XR_001746025.1:n.	N/A	Intron Variant
LOC101927245 transcript variant X12	XR_001746026.1:n.	N/A	Intron Variant
LOC101927245 transcript variant X4	XR_928481.2:n.	N/A	Intron Variant
LOC101927245 transcript variant X5	XR_928483.2:n.	N/A	Intron Variant
LOC101927245 transcript variant X10	XR_928489.2:n.	N/A	Intron Variant
LOC101927245 transcript variant X7	XR_001746023.1:n.	N/A	Genic Downstream Transcript Variant
LOC101927245 transcript variant X2	XR_928480.2:n.	N/A	Genic Downstream Transcript Variant
LOC101927245 transcript variant X6	XR_928482.2:n.	N/A	Genic Downstream Transcript Variant
LOC101927245 transcript variant X8	XR_928484.2:n.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.714	T=0.286
1000Genomes	American	Sub	694	C=0.700	T=0.300
1000Genomes	East Asian	Sub	1008	C=0.634	T=0.366
1000Genomes	Europe	Sub	1006	C=0.795	T=0.205
1000Genomes	Global	Study-wide	5008	C=0.712	T=0.288
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=0.777	T=0.223
The Genome Aggregation Database	African	Sub	8710	C=0.753	T=0.247
The Genome Aggregation Database	American	Sub	838	C=0.670	T=0.330
The Genome Aggregation Database	East Asian	Sub	1608	C=0.613	T=0.387
The Genome Aggregation Database	Europe	Sub	18498	C=0.783	T=0.216
The Genome Aggregation Database	Global	Study-wide	29956	C=0.762	T=0.237
The Genome Aggregation Database	Other	Sub	302	C=0.770	T=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.773	T=0.226
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.780	T=0.220

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

SNP ID	p-value	Traits	Study
rs2513929	0.000707	alcohol dependence	21314694

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

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr8	103740024	103740293	E067	25678
chr8	103740319	103742877	E067	25973
chr8	103751357	103751502	E067	37011
chr8	103751570	103751663	E067	37224
chr8	103751823	103751926	E067	37477
chr8	103740024	103740293	E068	25678
chr8	103740319	103742877	E068	25973
chr8	103751357	103751502	E068	37011
chr8	103751570	103751663	E068	37224
chr8	103751823	103751926	E068	37477
chr8	103761864	103762715	E068	47518
chr8	103674601	103675610	E069	-38736
chr8	103740024	103740293	E069	25678
chr8	103740319	103742877	E069	25973
chr8	103751357	103751502	E069	37011
chr8	103751570	103751663	E069	37224
chr8	103737620	103737967	E070	23274
chr8	103740319	103742877	E070	25973
chr8	103674242	103674282	E071	-40064
chr8	103674601	103675610	E071	-38736
chr8	103740024	103740293	E071	25678
chr8	103740319	103742877	E071	25973
chr8	103751357	103751502	E071	37011
chr8	103751570	103751663	E071	37224
chr8	103751823	103751926	E071	37477
chr8	103740319	103742877	E072	25973
chr8	103740319	103742877	E073	25973
chr8	103751357	103751502	E073	37011
chr8	103751570	103751663	E073	37224
chr8	103751823	103751926	E073	37477
chr8	103752138	103752951	E073	37792
chr8	103674601	103675610	E074	-38736
chr8	103740319	103742877	E074	25973
chr8	103757245	103758253	E074	42899
chr8	103740319	103742877	E081	25973
chr8	103740319	103742877	E082	25973

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	103665324	103671158	E067	-43188
chr8	103665324	103671158	E068	-43188
chr8	103665324	103671158	E069	-43188
chr8	103665324	103671158	E070	-43188
chr8	103665324	103671158	E071	-43188
chr8	103665324	103671158	E072	-43188
chr8	103665324	103671158	E073	-43188
chr8	103665324	103671158	E074	-43188
chr8	103665324	103671158	E082	-43188