rs431220

Homo sapiens
C>T
GAPLINC : Intron Variant
LOC105371965 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0049 (1481/29946,GnomAD)
T=0070 (2055/29118,TOPMED)
T=0052 (262/5008,1000G)
T=0010 (39/3854,ALSPAC)
T=0009 (32/3708,TWINSUK)
chr18:3467415 (GRCh38.p7) (18p11.31)
AD
GWASdb2
1   publication(s)
See rs on genome
24 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.3467415C>T
GRCh37.p13 chr 18NC_000018.9:g.3467413C>T

Gene: GAPLINC, gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNA(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GAPLINC transcript variant 2NR_110428.1:n.N/AIntron Variant
GAPLINC transcript variant 1NR_110429.1:n.N/AIntron Variant

Gene: LOC105371965, uncharacterized LOC105371965(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105371965 transcriptXR_935106.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.839T=0.161
1000GenomesAmericanSub694C=0.970T=0.030
1000GenomesEast AsianSub1008C=0.999T=0.001
1000GenomesEuropeSub1006C=0.980T=0.020
1000GenomesGlobalStudy-wide5008C=0.948T=0.052
1000GenomesSouth AsianSub978C=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.990T=0.010
The Genome Aggregation DatabaseAfricanSub8714C=0.853T=0.147
The Genome Aggregation DatabaseAmericanSub838C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1622C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18470C=0.990T=0.009
The Genome Aggregation DatabaseGlobalStudy-wide29946C=0.950T=0.049
The Genome Aggregation DatabaseOtherSub302C=0.990T=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.929T=0.070
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.991T=0.009
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
rs4312200.0000588alcoholismpha002891
rs4312200.0000588alcohol dependence20201924

eQTL of rs431220 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 rs431220 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 )
chr1834412723441696E067-25717
chr1834417983441945E067-25468
chr1834584503459907E067-7506
chr1834579593458368E068-9045
chr1834584503459907E068-7506
chr1835086053508706E06841192
chr1835087473508849E06841334
chr1835088963509642E06841483
chr1835118783512462E06844465
chr1835133593513409E06845946
chr1835134173513485E06846004
chr1834412723441696E069-25717
chr1834417983441945E069-25468
chr1834584503459907E069-7506
chr1834411303441201E071-26212
chr1834412723441696E071-25717
chr1834417983441945E071-25468
chr1834579593458368E071-9045
chr1834584503459907E071-7506
chr1834584503459907E072-7506
chr1835088963509642E07241483
chr1834579593458368E074-9045
chr1834584503459907E074-7506
chr1835087473508849E07441334






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1834464543457895E067-9518
chr1834988333500172E06731420
chr1834464543457895E068-9518
chr1834988333500172E06831420
chr1834464543457895E069-9518
chr1834988333500172E06931420
chr1834464543457895E070-9518
chr1834988333500172E07031420
chr1834464543457895E071-9518
chr1834988333500172E07131420
chr1834464543457895E072-9518
chr1834988333500172E07231420
chr1834464543457895E073-9518
chr1834988333500172E07331420
chr1834464543457895E074-9518
chr1834988333500172E07431420
chr1834464543457895E081-9518
chr1834464543457895E082-9518
chr1834988333500172E08231420