rs2028891

Homo sapiens
T>G
SCN2A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0484 (14450/29802,GnomAD)
T==0477 (13905/29118,TOPMED)
T==0493 (2470/5008,1000G)
G=0331 (1276/3854,ALSPAC)
G=0309 (1145/3708,TWINSUK)
chr2:165211148 (GRCh38.p7) (2q24.3)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
89 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.165211148T>G
GRCh37.p13 chr 2NC_000002.11:g.166067658T>G

Gene: SCN2A, sodium voltage-gated channel alpha subunit 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SCN2A transcript variant 2NM_001040142.1:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant 3NM_001040143.1:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant 1NM_021007.2:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X1XM_017004656.1:c.N/AIntron Variant
SCN2A transcript variant X2XM_005246753.3:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X6XM_005246755.4:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X1XM_017004655.1:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X3XM_017004657.1:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X4XM_017004658.1:c.N/AGenic Upstream Transcript Variant
SCN2A transcript variant X6XM_017004659.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.233G=0.767
1000GenomesAmericanSub694T=0.560G=0.440
1000GenomesEast AsianSub1008T=0.385G=0.615
1000GenomesEuropeSub1006T=0.662G=0.338
1000GenomesGlobalStudy-wide5008T=0.493G=0.507
1000GenomesSouth AsianSub978T=0.740G=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.669G=0.331
The Genome Aggregation DatabaseAfricanSub8704T=0.305G=0.695
The Genome Aggregation DatabaseAmericanSub830T=0.520G=0.480
The Genome Aggregation DatabaseEast AsianSub1574T=0.358G=0.642
The Genome Aggregation DatabaseEuropeSub18392T=0.623G=0.376
The Genome Aggregation DatabaseGlobalStudy-wide29802T=0.515G=0.484
The Genome Aggregation DatabaseOtherSub302T=0.780G=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.477G=0.522
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.691G=0.309
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs20288910.00014alcohol dependence24277619

eQTL of rs2028891 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 rs2028891 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 )
chr2166054872166055021E067-12637
chr2166033325166033666E069-33992
chr2166054872166055021E070-12637
chr2166057996166058067E070-9591
chr2166058147166058291E070-9367
chr2166054872166055021E081-12637
chr2166055117166055189E081-12469
chr2166058147166058291E081-9367
chr2166058480166058524E081-9134




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2166058940166059009E067-8649
chr2166059982166060043E067-7615
chr2166060110166060795E067-6863
chr2166095796166095999E06728138
chr2166096169166096309E06728511
chr2166096367166096627E06728709
chr2166096673166096777E06729015
chr2166096819166097007E06729161
chr2166097137166097219E06729479
chr2166097464166097574E06729806
chr2166097769166097819E06730111
chr2166058940166059009E068-8649
chr2166059982166060043E068-7615
chr2166060110166060795E068-6863
chr2166095796166095999E06828138
chr2166096169166096309E06828511
chr2166096367166096627E06828709
chr2166096673166096777E06829015
chr2166096819166097007E06829161
chr2166097137166097219E06829479
chr2166097464166097574E06829806
chr2166097769166097819E06830111
chr2166059982166060043E069-7615
chr2166060110166060795E069-6863
chr2166096169166096309E06928511
chr2166096367166096627E06928709
chr2166096673166096777E06929015
chr2166096819166097007E06929161
chr2166097137166097219E06929479
chr2166097464166097574E06929806
chr2166097769166097819E06930111
chr2166058940166059009E070-8649
chr2166059982166060043E070-7615
chr2166060110166060795E070-6863
chr2166059982166060043E071-7615
chr2166060110166060795E071-6863
chr2166095796166095999E07128138
chr2166096169166096309E07128511
chr2166096367166096627E07128709
chr2166096673166096777E07129015
chr2166096819166097007E07129161
chr2166097137166097219E07129479
chr2166097464166097574E07129806
chr2166097769166097819E07130111
chr2166058940166059009E072-8649
chr2166059982166060043E072-7615
chr2166060110166060795E072-6863
chr2166095796166095999E07228138
chr2166096169166096309E07228511
chr2166096367166096627E07228709
chr2166096673166096777E07229015
chr2166096819166097007E07229161
chr2166097137166097219E07229479
chr2166097464166097574E07229806
chr2166097769166097819E07230111
chr2166058940166059009E073-8649
chr2166059982166060043E073-7615
chr2166060110166060795E073-6863
chr2166095796166095999E07328138
chr2166096169166096309E07328511
chr2166096367166096627E07328709
chr2166096673166096777E07329015
chr2166096819166097007E07329161
chr2166097137166097219E07329479
chr2166097464166097574E07329806
chr2166097769166097819E07330111
chr2166060110166060795E074-6863
chr2166058940166059009E081-8649
chr2166059982166060043E081-7615
chr2166060110166060795E081-6863
chr2166095796166095999E08128138
chr2166096169166096309E08128511
chr2166096367166096627E08128709
chr2166096673166096777E08129015
chr2166096819166097007E08129161
chr2166097137166097219E08129479
chr2166097464166097574E08129806
chr2166097769166097819E08130111
chr2166058940166059009E082-8649
chr2166059982166060043E082-7615
chr2166060110166060795E082-6863
chr2166095796166095999E08228138
chr2166096169166096309E08228511
chr2166096367166096627E08228709
chr2166096673166096777E08229015
chr2166096819166097007E08229161
chr2166097137166097219E08229479
chr2166097464166097574E08229806
chr2166097769166097819E08230111