rs6874566

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LINC01331 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0341 (10208/29922,GnomAD)
C=0361 (10519/29118,TOPMED)
C=0351 (1760/5008,1000G)
C=0270 (1039/3854,ALSPAC)
C=0259 (961/3708,TWINSUK)

Position: chr5:74491055 (GRCh38.p7) (5q13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 64 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.74491055T>C
GRCh37.p13 chr 5	NC_000005.9:g.73786880T>C

Gene: LINC01331, long intergenic non-protein coding RNA 1331(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01331 transcript	NR_126354.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.515	C=0.485
1000Genomes	American	Sub	694	T=0.640	C=0.360
1000Genomes	East Asian	Sub	1008	T=0.753	C=0.247
1000Genomes	Europe	Sub	1006	T=0.728	C=0.272
1000Genomes	Global	Study-wide	5008	T=0.649	C=0.351
1000Genomes	South Asian	Sub	978	T=0.650	C=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.730	C=0.270
The Genome Aggregation Database	African	Sub	8706	T=0.541	C=0.459
The Genome Aggregation Database	American	Sub	834	T=0.700	C=0.300
The Genome Aggregation Database	East Asian	Sub	1618	T=0.784	C=0.216
The Genome Aggregation Database	Europe	Sub	18462	T=0.701	C=0.298
The Genome Aggregation Database	Global	Study-wide	29922	T=0.658	C=0.341
The Genome Aggregation Database	Other	Sub	302	T=0.700	C=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.638	C=0.361
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.741	C=0.259

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

SNP ID	p-value	Traits	Study
rs6874566	0.000874	alcohol dependence	24277619

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 )
chr5	73778372	73778641	E067	-8239
chr5	73778950	73779144	E067	-7736
chr5	73833696	73833919	E068	46816
chr5	73834005	73834512	E068	47125
chr5	73756713	73756794	E070	-30086
chr5	73757023	73757063	E070	-29817
chr5	73757130	73757622	E070	-29258
chr5	73758002	73758057	E070	-28823
chr5	73758285	73758478	E070	-28402
chr5	73763839	73763927	E070	-22953
chr5	73764693	73764787	E070	-22093
chr5	73764898	73764954	E070	-21926
chr5	73765458	73765636	E070	-21244
chr5	73765678	73765821	E070	-21059
chr5	73766264	73766324	E070	-20556
chr5	73766387	73766644	E070	-20236
chr5	73772320	73772635	E070	-14245
chr5	73772668	73772718	E070	-14162
chr5	73772989	73773066	E070	-13814
chr5	73778372	73778641	E070	-8239
chr5	73787819	73787892	E070	939
chr5	73787933	73788617	E070	1053
chr5	73795043	73795432	E070	8163
chr5	73795462	73795777	E070	8582
chr5	73795913	73796384	E070	9033
chr5	73796438	73796677	E070	9558
chr5	73803205	73803521	E070	16325
chr5	73803598	73803698	E070	16718
chr5	73803734	73804406	E070	16854
chr5	73831847	73832120	E070	44967
chr5	73832195	73832245	E070	45315
chr5	73832361	73832528	E070	45481
chr5	73778372	73778641	E071	-8239
chr5	73778372	73778641	E072	-8239
chr5	73778950	73779144	E072	-7736
chr5	73795462	73795777	E072	8582
chr5	73795913	73796384	E072	9033
chr5	73818205	73818396	E072	31325
chr5	73813214	73813391	E073	26334
chr5	73814083	73814167	E073	27203
chr5	73778950	73779144	E074	-7736
chr5	73757023	73757063	E081	-29817
chr5	73765458	73765636	E081	-21244
chr5	73765678	73765821	E081	-21059
chr5	73766264	73766324	E081	-20556
chr5	73766387	73766644	E081	-20236
chr5	73771951	73772222	E081	-14658
chr5	73772320	73772635	E081	-14245
chr5	73772668	73772718	E081	-14162
chr5	73772989	73773066	E081	-13814
chr5	73795462	73795777	E081	8582
chr5	73795913	73796384	E081	9033
chr5	73796438	73796677	E081	9558
chr5	73756713	73756794	E082	-30086
chr5	73757023	73757063	E082	-29817
chr5	73757130	73757622	E082	-29258
chr5	73758002	73758057	E082	-28823
chr5	73765458	73765636	E082	-21244
chr5	73765678	73765821	E082	-21059
chr5	73771951	73772222	E082	-14658
chr5	73772320	73772635	E082	-14245
chr5	73772668	73772718	E082	-14162
chr5	73772989	73773066	E082	-13814
chr5	73778372	73778641	E082	-8239

rs6874566

Genomic Coordinates

Gene: LINC01331, long intergenic non-protein coding RNA 1331(minus strand)

Population Frequency

P-Value

eQTL of rs6874566 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6874566 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)