rs12476319

Homo sapiens
T>C
GREB1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0487 (14575/29910,GnomAD)
C=0439 (12804/29116,TOPMED)
T==0454 (2273/5008,1000G)
C=0493 (1900/3854,ALSPAC)
C=0471 (1747/3708,TWINSUK)
chr2:11608280 (GRCh38.p7) (2p25.1)
AD
GWASdb2
1   publication(s)
See rs on genome
43 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.11608280T>C
GRCh37.p13 chr 2NC_000002.11:g.11748406T>C
GREB1 RefSeqGeneNG_029429.1:g.79165T>C

Gene: GREB1, growth regulation by estrogen in breast cancer 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GREB1 transcript variant aNM_014668.3:c.N/AIntron Variant
GREB1 transcript variant bNM_033090.2:c.N/AGenic Downstream Transcript Variant
GREB1 transcript variant cNM_148903.2:c.N/AGenic Downstream Transcript Variant
GREB1 transcript variant X2XM_005246192.4:c.N/AIntron Variant
GREB1 transcript variant X13XM_005246196.3:c.N/AIntron Variant
GREB1 transcript variant X3XM_011510418.2:c.N/AIntron Variant
GREB1 transcript variant X2XM_011510419.2:c.N/AIntron Variant
GREB1 transcript variant X12XM_011510422.2:c.N/AIntron Variant
GREB1 transcript variant X8XM_011510423.2:c.N/AGenic Downstream Transcript Variant
GREB1 transcript variant X4XR_001739081.1:n.N/AIntron Variant
GREB1 transcript variant X7XR_922686.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.595C=0.405
1000GenomesAmericanSub694T=0.550C=0.450
1000GenomesEast AsianSub1008T=0.300C=0.700
1000GenomesEuropeSub1006T=0.527C=0.473
1000GenomesGlobalStudy-wide5008T=0.454C=0.546
1000GenomesSouth AsianSub978T=0.280C=0.720
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.507C=0.493
The Genome Aggregation DatabaseAfricanSub8686T=0.592C=0.408
The Genome Aggregation DatabaseAmericanSub834T=0.580C=0.420
The Genome Aggregation DatabaseEast AsianSub1618T=0.311C=0.689
The Genome Aggregation DatabaseEuropeSub18470T=0.490C=0.509
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.512C=0.487
The Genome Aggregation DatabaseOtherSub302T=0.470C=0.530
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.560C=0.439
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.529C=0.471
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs124763190.0005alcohol dependence21314694

eQTL of rs12476319 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 rs12476319 in Fetal Brain

Probe ID Position Gene beta p-value
cg07314298chr2:11723111GREB10.06169907276669421.6525e-9

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 )
chr21172276311723626E067-24780
chr21172403511724158E067-24248
chr21172416111724885E067-23521
chr21175264411752718E0674238
chr21176133511762002E06712929
chr21172276311723626E068-24780
chr21172403511724158E068-24248
chr21172416111724885E068-23521
chr21176133511762002E06812929
chr21170678811706873E069-41533
chr21170714111707185E069-41221
chr21172416111724885E069-23521
chr21179324611793290E06944840
chr21172276311723626E071-24780
chr21172403511724158E071-24248
chr21172416111724885E071-23521
chr21175264411752718E0714238
chr21176133511762002E07112929
chr21169906711699244E072-49162
chr21170653611706614E072-41792
chr21170678811706873E072-41533
chr21170714111707185E072-41221
chr21170730011707351E072-41055
chr21172210511722220E072-26186
chr21172227711722627E072-25779
chr21172276311723626E072-24780
chr21172403511724158E072-24248
chr21172416111724885E072-23521
chr21176133511762002E07212929
chr21179808711798174E07249681
chr21171088811710934E073-37472
chr21171098111711050E073-37356
chr21171110711711152E073-37254
chr21170678811706873E074-41533
chr21170714111707185E074-41221
chr21176133511762002E07412929
chr21179203311792415E07443627
chr21179203311792415E08143627
chr21179274511792992E08144339
chr21179324611793290E08144840
chr21179203311792415E08243627
chr21179274511792992E08244339
chr21179324611793290E08244840