rs12920919

Homo sapiens
T>C
GRIN2A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0322 (9649/29912,GnomAD)
C=0321 (9357/29118,TOPMED)
C=0264 (1321/5008,1000G)
C=0360 (1387/3854,ALSPAC)
C=0341 (1264/3708,TWINSUK)
chr16:9844123 (GRCh38.p7) (16p13.2)
ND
GWASdb2
1   publication(s)
See rs on genome
98 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.9844123T>C
GRCh37.p13 chr 16NC_000016.9:g.9937980T>C
GRIN2A RefSeqGeneNG_011812.1:g.343632A>G

Gene: GRIN2A, glutamate ionotropic receptor NMDA type subunit 2A(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GRIN2A transcript variant 2NM_000833.4:c.N/AIntron Variant
GRIN2A transcript variant 1NM_001134407.2:c.N/AIntron Variant
GRIN2A transcript variant 3NM_001134408.2:c.N/AIntron Variant
GRIN2A transcript variant X3XM_011522458.2:c.N/AIntron Variant
GRIN2A transcript variant X4XM_011522461.2:c.N/AIntron Variant
GRIN2A transcript variant X1XM_017023172.1:c.N/AIntron Variant
GRIN2A transcript variant X2XM_017023173.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.685C=0.315
1000GenomesAmericanSub694T=0.750C=0.250
1000GenomesEast AsianSub1008T=0.877C=0.123
1000GenomesEuropeSub1006T=0.651C=0.349
1000GenomesGlobalStudy-wide5008T=0.736C=0.264
1000GenomesSouth AsianSub978T=0.740C=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.640C=0.360
The Genome Aggregation DatabaseAfricanSub8696T=0.669C=0.331
The Genome Aggregation DatabaseAmericanSub836T=0.750C=0.250
The Genome Aggregation DatabaseEast AsianSub1620T=0.875C=0.125
The Genome Aggregation DatabaseEuropeSub18458T=0.661C=0.339
The Genome Aggregation DatabaseGlobalStudy-wide29912T=0.677C=0.322
The Genome Aggregation DatabaseOtherSub302T=0.680C=0.320
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.678C=0.321
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.659C=0.341
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs129209190.0001nicotine smoking19268276

eQTL of rs12920919 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 rs12920919 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 )
chr1699068329906900E067-31080
chr1699142219914302E067-23678
chr1699143129915256E067-22724
chr1699152609915328E067-22652
chr1699155689915661E067-22319
chr1699158489916180E067-21800
chr1699394889939538E0671508
chr1699635779963627E06725597
chr1699636869963971E06725706
chr1699639809964153E06726000
chr1699790359979085E06741055
chr1699140559914121E068-23859
chr1699142219914302E068-23678
chr1699143129915256E068-22724
chr1699152609915328E068-22652
chr1699155689915661E068-22319
chr1699224419922496E068-15484
chr1699227589922818E068-15162
chr1699391349939256E0681154
chr1699392909939340E0681310
chr1699393529939472E0681372
chr1699394889939538E0681508
chr1699790359979085E06841055
chr1699791549979782E06841174
chr1699798159980086E06841835
chr1698948119894870E069-43110
chr1698951159895170E069-42810
chr1699066619906711E069-31269
chr1699067309906781E069-31199
chr1699140559914121E069-23859
chr1699142219914302E069-23678
chr1699143129915256E069-22724
chr1699152609915328E069-22652
chr1699155689915661E069-22319
chr1699408939941116E0692913
chr1699790359979085E06941055
chr1699798159980086E06941835
chr1698990329899292E070-38688
chr1698993309899387E070-38593
chr1699112079911302E070-26678
chr1699138309913936E070-24044
chr1699140559914121E070-23859
chr1699142219914302E070-23678
chr1699143129915256E070-22724
chr1699152609915328E070-22652
chr1699155689915661E070-22319
chr1699235359923636E070-14344
chr1699237239923996E070-13984
chr1699240549924293E070-13687
chr1699245099924564E070-13416
chr1699246569924822E070-13158
chr1699249319924981E070-12999
chr1699308879930992E070-6988
chr1699310319931085E070-6895
chr1699560399956172E07018059
chr1699563669956416E07018386
chr1699140559914121E071-23859
chr1699142219914302E071-23678
chr1699143129915256E071-22724
chr1699152609915328E071-22652
chr1699155689915661E071-22319
chr1699697849969864E07131804
chr1699698729969922E07131892
chr1699790359979085E07141055
chr1699798159980086E07141835
chr1699140559914121E072-23859
chr1699142219914302E072-23678
chr1699143129915256E072-22724
chr1699152609915328E072-22652
chr1699155689915661E072-22319
chr1699182539918330E072-19650
chr1699184269918529E072-19451
chr1699185429918592E072-19388
chr1699408939941116E0722913
chr1699411399941250E0723159
chr1699790359979085E07241055
chr1699142219914302E073-23678
chr1699143129915256E073-22724
chr1699152609915328E073-22652
chr1699314289931672E073-6308
chr1699790359979085E07341055
chr1699791549979782E07341174
chr1699140559914121E074-23859
chr1699142219914302E074-23678
chr1699143129915256E074-22724
chr1699152609915328E074-22652
chr1699155689915661E074-22319
chr1699143129915256E081-22724
chr1699240549924293E081-13687
chr1699245099924564E081-13416
chr1699246569924822E081-13158
chr1699249319924981E081-12999
chr1699483459949001E08110365
chr1699790359979085E08141055
chr1699791549979782E08141174
chr1699140559914121E082-23859
chr1699142219914302E082-23678
chr1699791549979782E08241174