rs62184317

Homo sapiens
C>T
C2orf88 : Intron Variant
LOC105373795 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0124 (3715/29926,GnomAD)
T=0107 (3125/29118,TOPMED)
T=0092 (460/5008,1000G)
T=0181 (696/3854,ALSPAC)
T=0176 (651/3708,TWINSUK)
chr2:189917038 (GRCh38.p7) (2q32.2)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.189917038C>T
GRCh37.p13 chr 2NC_000002.11:g.190781764C>T

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

Molecule type Change Amino acid[Codon] SO Term
C2orf88 transcript variant 1NM_001042519.1:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant 3NM_001042520.1:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant 2NM_001042521.1:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant 4NM_032321.2:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant X1XM_005246905.1:c.N/AIntron Variant
C2orf88 transcript variant X2XM_011511982.1:c.N/AIntron Variant
C2orf88 transcript variant X6XM_011511986.2:c.N/AIntron Variant
C2orf88 transcript variant X7XM_006712795.2:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant X3XM_011511983.1:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant X4XM_011511984.2:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant X5XM_011511985.2:c.N/AGenic Upstream Transcript Variant
C2orf88 transcript variant X7XM_017005096.1:c.N/AGenic Upstream Transcript Variant

Gene: LOC105373795, uncharacterized LOC105373795(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105373795 transcriptXR_923695.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.988T=0.012
1000GenomesAmericanSub694C=0.850T=0.150
1000GenomesEast AsianSub1008C=0.925T=0.075
1000GenomesEuropeSub1006C=0.816T=0.184
1000GenomesGlobalStudy-wide5008C=0.908T=0.092
1000GenomesSouth AsianSub978C=0.920T=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.819T=0.181
The Genome Aggregation DatabaseAfricanSub8716C=0.962T=0.038
The Genome Aggregation DatabaseAmericanSub836C=0.910T=0.090
The Genome Aggregation DatabaseEast AsianSub1618C=0.925T=0.075
The Genome Aggregation DatabaseEuropeSub18454C=0.830T=0.169
The Genome Aggregation DatabaseGlobalStudy-wide29926C=0.875T=0.124
The Genome Aggregation DatabaseOtherSub302C=0.800T=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.892T=0.107
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.824T=0.176
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs621843173.81E-06alcohol dependence (age at onset)24962325

eQTL of rs62184317 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:190781764ORMDL1ENSG00000128699.9C>T2.7066e-14132667Cerebellum
Chr2:190781764ASNSD1ENSG00000138381.5C>T1.1310e-15255653Frontal_Cortex_BA9
Chr2:190781764OSGEPL1-AS1ENSG00000253559.1C>T6.6669e-4152183Hypothalamus
Chr2:190781764ASNSD1ENSG00000138381.5C>T7.9557e-16255653Cortex
Chr2:190781764RP11-455J20.3ENSG00000273240.1C>T2.9653e-10152582Cortex
Chr2:190781764ORMDL1ENSG00000128699.9C>T1.8618e-5132667Cerebellar_Hemisphere
Chr2:190781764ASNSD1ENSG00000138381.5C>T6.1937e-14255653Nucleus_accumbens_basal_ganglia

meQTL of rs62184317 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.