rs3897230

Homo sapiens
C>T
LOC102723490 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0225 (6735/29932,GnomAD)
T=0190 (5550/29116,TOPMED)
T=0141 (708/5008,1000G)
T=0281 (1084/3854,ALSPAC)
T=0279 (1036/3708,TWINSUK)
chr13:36773840 (GRCh38.p7) (13q13.3)
AD
GWASdb2
1   publication(s)
See rs on genome
39 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.36773840C>T
GRCh37.p13 chr 13NC_000013.10:g.37347977C>T

Gene: LOC102723490, uncharacterized LOC102723490(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC102723490 transcript variant X2XR_001749823.1:n.N/AIntron Variant
LOC102723490 transcript variant X2XR_001749824.1:n.N/AIntron Variant
LOC102723490 transcript variant X5XR_001749825.1:n.N/AIntron Variant
LOC102723490 transcript variant X9XR_001749828.1:n.N/AIntron Variant
LOC102723490 transcript variant X7XR_001749829.1:n.N/AIntron Variant
LOC102723490 transcript variant X8XR_001749830.1:n.N/AIntron Variant
LOC102723490 transcript variant X11XR_001749832.1:n.N/AIntron Variant
LOC102723490 transcript variant X1XR_941857.2:n.N/AIntron Variant
LOC102723490 transcript variant X5XR_001749826.1:n.N/AGenic Upstream Transcript Variant
LOC102723490 transcript variant X9XR_001749831.1:n.N/AGenic Upstream Transcript Variant
LOC102723490 transcript variant X10XR_941872.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.900T=0.100
1000GenomesAmericanSub694C=0.740T=0.260
1000GenomesEast AsianSub1008C=0.969T=0.031
1000GenomesEuropeSub1006C=0.724T=0.276
1000GenomesGlobalStudy-wide5008C=0.859T=0.141
1000GenomesSouth AsianSub978C=0.910T=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.719T=0.281
The Genome Aggregation DatabaseAfricanSub8722C=0.874T=0.126
The Genome Aggregation DatabaseAmericanSub834C=0.710T=0.290
The Genome Aggregation DatabaseEast AsianSub1616C=0.975T=0.025
The Genome Aggregation DatabaseEuropeSub18458C=0.712T=0.288
The Genome Aggregation DatabaseGlobalStudy-wide29932C=0.775T=0.225
The Genome Aggregation DatabaseOtherSub302C=0.870T=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.809T=0.190
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.721T=0.279
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs38972300.00071alcohol dependence20201924

eQTL of rs3897230 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 rs3897230 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 )
chr133739526237395319E06747285
chr133739548637395537E06747509
chr133739557337395721E06747596
chr133739700237397132E06749025
chr133739714437397184E06749167
chr133739721237397301E06749235
chr133737834937378435E06830372
chr133739526237395319E06847285
chr133739548637395537E06847509
chr133739557337395721E06847596
chr133739591537395979E07047938
chr133739607737396179E07048100
chr133739661837396668E07048641
chr133739747437397514E07049497
chr133739789037397940E07049913
chr133739230337392495E07144326
chr133739526237395319E07147285
chr133739548637395537E07147509
chr133739557337395721E07147596
chr133739591537395979E07147938
chr133739700237397132E07149025
chr133739714437397184E07149167
chr133739721237397301E07149235
chr133739230337392495E07444326
chr133739526237395319E07447285
chr133739526237395319E08147285
chr133739548637395537E08147509
chr133739557337395721E08147596
chr133739591537395979E08147938
chr133739607737396179E08148100
chr133739661837396668E08148641
chr133739700237397132E08149025
chr133739714437397184E08149167
chr133739721237397301E08149235
chr133739591537395979E08247938
chr133739700237397132E08249025
chr133739714437397184E08249167
chr133739721237397301E08249235
chr133739747437397514E08249497







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr133739252837394597E06744551
chr133739252837394597E06844551
chr133739252837394597E06944551
chr133739252837394597E07044551
chr133739252837394597E07144551
chr133739252837394597E07244551
chr133739252837394597E07344551
chr133739252837394597E07444551
chr133739252837394597E08244551