rs2677112

Homo sapiens
T>G
USH2A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0435 (13026/29928,GnomAD)
G=0343 (10005/29116,TOPMED)
G=0286 (1432/5008,1000G)
T==0432 (1665/3854,ALSPAC)
T==0434 (1611/3708,TWINSUK)
chr1:215651825 (GRCh38.p7) (1q41)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.215651825T>G
GRCh37.p13 chr 1NC_000001.10:g.215825167T>G
USH2A RefSeqGeneNG_009497.1:g.776572A>C

Gene: USH2A, Usher syndrome 2A (autosomal recessive, mild)(minus strand)

Molecule type Change Amino acid[Codon] SO Term
USH2A transcript variant 2NM_206933.2:c.N/AIntron Variant
USH2A transcript variant 1NM_007123.5:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.975G=0.025
1000GenomesAmericanSub694T=0.520G=0.480
1000GenomesEast AsianSub1008T=0.705G=0.295
1000GenomesEuropeSub1006T=0.464G=0.536
1000GenomesGlobalStudy-wide5008T=0.714G=0.286
1000GenomesSouth AsianSub978T=0.770G=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.432G=0.568
The Genome Aggregation DatabaseAfricanSub8724T=0.898G=0.102
The Genome Aggregation DatabaseAmericanSub836T=0.530G=0.470
The Genome Aggregation DatabaseEast AsianSub1614T=0.657G=0.343
The Genome Aggregation DatabaseEuropeSub18452T=0.400G=0.599
The Genome Aggregation DatabaseGlobalStudy-wide29928T=0.564G=0.435
The Genome Aggregation DatabaseOtherSub302T=0.550G=0.450
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.656G=0.343
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.434G=0.566
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs26771120.000856alcohol dependence21314694

eQTL of rs2677112 in Brain tissues (GTEx Analysis Release V7)

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

meQTL of rs2677112 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.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr1215785856215786011E070-39156
chr1215778357215778951E071-46216
chr1215778965215779015E073-46152
chr1215778357215778951E074-46216