rs1321075

Homo sapiens
T>G
RUNX2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0166 (4855/29118,TOPMED)
T==0177 (884/5008,1000G)
T==0140 (541/3854,ALSPAC)
T==0146 (543/3708,TWINSUK)
chr6:45424206 (GRCh38.p7) (6p21.1)
AD
GWASdb2
5   publication(s)
See rs on genome
47 Enhancers around
33 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.45424206T>G
GRCh37.p13 chr 6NC_000006.11:g.45391943T>G
RUNX2 RefSeqGeneNG_008020.1:g.100890T>G

Gene: RUNX2, runt related transcription factor 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RUNX2 transcript variant 2NM_001015051.3:c.N/AIntron Variant
RUNX2 transcript variant 1NM_001024630.3:c.N/AIntron Variant
RUNX2 transcript variant 4NM_001278478.1:c.N/AIntron Variant
RUNX2 transcript variant 5NR_103532.1:n.N/AGenic Downstream Transcript Variant
RUNX2 transcript variant 6NR_103533.1:n.N/AGenic Downstream Transcript Variant
RUNX2 transcript variant X8XM_006715232.1:c.N/AIntron Variant
RUNX2 transcript variant X1XM_011514960.2:c.N/AIntron Variant
RUNX2 transcript variant X3XM_011514961.2:c.N/AIntron Variant
RUNX2 transcript variant X4XM_011514962.2:c.N/AIntron Variant
RUNX2 transcript variant X5XM_011514963.2:c.N/AIntron Variant
RUNX2 transcript variant X7XM_011514964.2:c.N/AIntron Variant
RUNX2 transcript variant X10XM_011514965.2:c.N/AIntron Variant
RUNX2 transcript variant X2XM_017011391.1:c.N/AIntron Variant
RUNX2 transcript variant X6XM_017011392.1:c.N/AIntron Variant
RUNX2 transcript variant X9XM_017011393.1:c.N/AIntron Variant
RUNX2 transcript variant X13XM_017011394.1:c.N/AIntron Variant
RUNX2 transcript variant X14XM_017011395.1:c.N/AIntron Variant
RUNX2 transcript variant X16XM_017011396.1:c.N/AIntron Variant
RUNX2 transcript variant X11XM_011514966.2:c.N/AGenic Upstream Transcript Variant
RUNX2 transcript variant X15XR_001743701.1:n.N/AIntron Variant
RUNX2 transcript variant X12XR_926323.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.166G=0.834
1000GenomesAmericanSub694T=0.280G=0.720
1000GenomesEast AsianSub1008T=0.242G=0.758
1000GenomesEuropeSub1006T=0.163G=0.837
1000GenomesGlobalStudy-wide5008T=0.177G=0.823
1000GenomesSouth AsianSub978T=0.060G=0.940
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.140G=0.860
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.166G=0.833
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.146G=0.854
PMID Title Author Journal
21088106Associations between genetic variation in RUNX1, RUNX2, RUNX3, MAPK1 and eIF4E and riskof colon and rectal cancer: additional support for a TGF-beta-signaling pathway.Slattery MLCarcinogenesis
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry
20721706RUNX2 polymorphisms associated with OPLL and OLF in the Han population.Liu YClin Orthop Relat Res
26960368Association Between Dentin Matrix Protein 1 (rs10019009) Polymorphism and Ankylosing Spondylitis in a Chinese Han Population from Shandong Province.Liu JMChin Med J (Engl)
27704615Role of Runx2 polymorphisms in risk and prognosis of ossification of posterior longitudinal ligament.Chang FJ Clin Lab Anal

P-Value

SNP ID p-value Traits Study
rs13210759.2E-05alcoholism (heaviness of drinking)21529783

eQTL of rs1321075 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 rs1321075 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 )
chr64534691745347053E067-44890
chr64540443745405216E06712494
chr64540525445405394E06713311
chr64540546845405584E06713525
chr64541318545414237E06721242
chr64544016145440447E06748218
chr64544044845440653E06748505
chr64541318545414237E06821242
chr64544016145440447E06848218
chr64544044845440653E06848505
chr64540443745405216E06912494
chr64540525445405394E06913311
chr64540546845405584E06913525
chr64541318545414237E06921242
chr64544016145440447E06948218
chr64544044845440653E06948505
chr64534383545343972E070-47971
chr64541318545414237E07021242
chr64534321745343407E071-48536
chr64534383545343972E071-47971
chr64534691745347053E071-44890
chr64540443745405216E07112494
chr64540525445405394E07113311
chr64540546845405584E07113525
chr64541626945416321E07124326
chr64544016145440447E07148218
chr64544044845440653E07148505
chr64534691745347053E072-44890
chr64541318545414237E07221242
chr64544016145440447E07248218
chr64544044845440653E07248505
chr64540660945407136E07314666
chr64540443745405216E07412494
chr64540525445405394E07413311
chr64540546845405584E07413525
chr64541318545414237E07421242
chr64544016145440447E07448218
chr64544044845440653E07448505
chr64544093945441260E07448996
chr64544151245441623E07449569
chr64534691745347053E081-44890
chr64541318545414237E08121242
chr64541427945414346E08122336
chr64541481845414885E08122875
chr64541495545415006E08123012
chr64541561245415684E08123669
chr64541318545414237E08221242










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr64534406845346664E067-45279
chr64538714245387853E067-4090
chr64538786345387948E067-3995
chr64538795345392155E0670
chr64534406845346664E068-45279
chr64538714245387853E068-4090
chr64538786345387948E068-3995
chr64538795345392155E0680
chr64539222245392594E068279
chr64534406845346664E069-45279
chr64538786345387948E069-3995
chr64538795345392155E0690
chr64539222245392594E069279
chr64534406845346664E070-45279
chr64534406845346664E071-45279
chr64539222245392594E071279
chr64534406845346664E072-45279
chr64538714245387853E072-4090
chr64538786345387948E072-3995
chr64538795345392155E0720
chr64534406845346664E073-45279
chr64538714245387853E073-4090
chr64538786345387948E073-3995
chr64538795345392155E0730
chr64539222245392594E073279
chr64534406845346664E074-45279
chr64538714245387853E074-4090
chr64538786345387948E074-3995
chr64538795345392155E0740
chr64534406845346664E081-45279
chr64534406845346664E082-45279
chr64538786345387948E082-3995
chr64538795345392155E0820