rs7563391

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

C2orf88 : Intron Variant
LOC105373795 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0152 (4578/29936,GnomAD)
C=0147 (4296/29118,TOPMED)
C=0118 (590/5008,1000G)
C=0184 (710/3854,ALSPAC)
C=0179 (663/3708,TWINSUK)

Position: chr2:189915077 (GRCh38.p7) (2q32.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.189915077G>C
GRCh37.p13 chr 2	NC_000002.11:g.190779803G>C

Gene: C2orf88, chromosome 2 open reading frame 88(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C2orf88 transcript variant 1	NM_001042519.1:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant 3	NM_001042520.1:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant 2	NM_001042521.1:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant 4	NM_032321.2:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant X1	XM_005246905.1:c.	N/A	Intron Variant
C2orf88 transcript variant X2	XM_011511982.1:c.	N/A	Intron Variant
C2orf88 transcript variant X6	XM_011511986.2:c.	N/A	Intron Variant
C2orf88 transcript variant X7	XM_006712795.2:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant X3	XM_011511983.1:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant X4	XM_011511984.2:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant X5	XM_011511985.2:c.	N/A	Genic Upstream Transcript Variant
C2orf88 transcript variant X7	XM_017005096.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC105373795, uncharacterized LOC105373795(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373795 transcript	XR_923695.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.894	C=0.106
1000Genomes	American	Sub	694	G=0.840	C=0.160
1000Genomes	East Asian	Sub	1008	G=0.925	C=0.075
1000Genomes	Europe	Sub	1006	G=0.813	C=0.187
1000Genomes	Global	Study-wide	5008	G=0.882	C=0.118
1000Genomes	South Asian	Sub	978	G=0.920	C=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.816	C=0.184
The Genome Aggregation Database	African	Sub	8716	G=0.877	C=0.123
The Genome Aggregation Database	American	Sub	838	G=0.900	C=0.100
The Genome Aggregation Database	East Asian	Sub	1618	G=0.925	C=0.075
The Genome Aggregation Database	Europe	Sub	18464	G=0.824	C=0.175
The Genome Aggregation Database	Global	Study-wide	29936	G=0.847	C=0.152
The Genome Aggregation Database	Other	Sub	300	G=0.790	C=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.852	C=0.147
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.821	C=0.179

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs7563391	3.81E-06	alcohol dependence (age at onset)	24962325

eQTL of rs7563391 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:190779803	ORMDL1	ENSG00000128699.9	G>C	2.7066e-14	130706	Cerebellum
Chr2:190779803	ASNSD1	ENSG00000138381.5	G>C	1.1310e-15	253692	Frontal_Cortex_BA9
Chr2:190779803	OSGEPL1-AS1	ENSG00000253559.1	G>C	6.6669e-4	150222	Hypothalamus
Chr2:190779803	ASNSD1	ENSG00000138381.5	G>C	7.9557e-16	253692	Cortex
Chr2:190779803	RP11-455J20.3	ENSG00000273240.1	G>C	2.9653e-10	150621	Cortex
Chr2:190779803	ORMDL1	ENSG00000128699.9	G>C	1.8618e-5	130706	Cerebellar_Hemisphere
Chr2:190779803	ASNSD1	ENSG00000138381.5	G>C	6.2798e-13	253692	Caudate_basal_ganglia
Chr2:190779803	ASNSD1	ENSG00000138381.5	G>C	6.1937e-14	253692	Nucleus_accumbens_basal_ganglia

meQTL of rs7563391 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.