rs2216712

Homo sapiens
C>T
LOC105374728 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0138 (4131/29912,GnomAD)
T=0141 (4111/29118,TOPMED)
T=0118 (592/5008,1000G)
T=0136 (525/3854,ALSPAC)
T=0136 (506/3708,TWINSUK)
chr5:37918601 (GRCh38.p7) (5p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.37918601C>T
GRCh37.p13 chr 5NC_000005.9:g.37918703C>T

Gene: LOC105374728, uncharacterized LOC105374728(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02117 transcript variant X1XR_925922.2:n.811G>AG>ANon Coding Transcript Variant
LINC02117 transcript variant X2XR_925923.2:n.795G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.856T=0.144
1000GenomesAmericanSub694C=0.800T=0.200
1000GenomesEast AsianSub1008C=0.936T=0.064
1000GenomesEuropeSub1006C=0.892T=0.108
1000GenomesGlobalStudy-wide5008C=0.882T=0.118
1000GenomesSouth AsianSub978C=0.910T=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.864T=0.136
The Genome Aggregation DatabaseAfricanSub8700C=0.833T=0.167
The Genome Aggregation DatabaseAmericanSub830C=0.790T=0.210
The Genome Aggregation DatabaseEast AsianSub1614C=0.944T=0.056
The Genome Aggregation DatabaseEuropeSub18466C=0.871T=0.128
The Genome Aggregation DatabaseGlobalStudy-wide29912C=0.861T=0.138
The Genome Aggregation DatabaseOtherSub302C=0.840T=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.858T=0.141
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.864T=0.136
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs22167127.9E-06alcoholism (heaviness of drinking)21529783

eQTL of rs2216712 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 rs2216712 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 )
chr53790090437901086E067-17617
chr53788641237886888E070-31815
chr53788641237886888E074-31815