rs2253319

Homo sapiens
C>T
RUNX1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0375 (11214/29846,GnomAD)
T=0418 (12180/29118,TOPMED)
T=0434 (2172/5008,1000G)
T=0325 (1253/3854,ALSPAC)
T=0324 (1201/3708,TWINSUK)
chr21:34815749 (GRCh38.p7) (21q22.12)
ND
GWASdb2
5   publication(s)
See rs on genome
7 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.34815749C>T
GRCh37.p13 chr 21NC_000021.8:g.36188046C>T
RUNX1 RefSeqGene LRG_482

Gene: RUNX1, runt related transcription factor 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
RUNX1 transcript variant 2NM_001001890.2:c.N/AIntron Variant
RUNX1 transcript variant 1NM_001754.4:c.N/AIntron Variant
RUNX1 transcript variant 3NM_001122607.1:c.N/AGenic Downstream Transcript Variant
RUNX1 transcript variant X2XM_005261068.3:c.N/AIntron Variant
RUNX1 transcript variant X5XM_005261069.4:c.N/AIntron Variant
RUNX1 transcript variant X1XM_011529766.2:c.N/AIntron Variant
RUNX1 transcript variant X3XM_011529767.2:c.N/AIntron Variant
RUNX1 transcript variant X6XM_011529768.2:c.N/AIntron Variant
RUNX1 transcript variant X4XM_017028487.1:c.N/AIntron Variant
RUNX1 transcript variant X8XM_011529770.2:c.N/AGenic Downstream Transcript Variant
RUNX1 transcript variant X7XR_937576.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.419T=0.581
1000GenomesAmericanSub694C=0.660T=0.340
1000GenomesEast AsianSub1008C=0.583T=0.417
1000GenomesEuropeSub1006C=0.670T=0.330
1000GenomesGlobalStudy-wide5008C=0.566T=0.434
1000GenomesSouth AsianSub978C=0.570T=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.675T=0.325
The Genome Aggregation DatabaseAfricanSub8688C=0.449T=0.551
The Genome Aggregation DatabaseAmericanSub836C=0.650T=0.350
The Genome Aggregation DatabaseEast AsianSub1606C=0.641T=0.359
The Genome Aggregation DatabaseEuropeSub18416C=0.703T=0.296
The Genome Aggregation DatabaseGlobalStudy-wide29846C=0.624T=0.375
The Genome Aggregation DatabaseOtherSub300C=0.700T=0.300
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.581T=0.418
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.676T=0.324
PMID Title Author Journal
21365634Genetic variation in the transforming growth factor-beta signaling pathway and survival after diagnosis with colon and rectal cancer.Slattery MLCancer
20735389Clinical significance of runt-related transcription factor 1 polymorphism in prostate cancer.Huang SPBJU Int
22212731A polymorphism in the thyroid hormone receptor gene is associated with bronchodilator response in asthmatics.Duan QLPharmacogenomics J
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet
17903305A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.Murabito JMBMC Med Genet

P-Value

SNP ID p-value Traits Study
rs22533190.000296nicotine smoking19268276

eQTL of rs2253319 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 rs2253319 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 )
chr213621628736217518E07028241
chr213622004836220282E07032002
chr213622030836220413E07032262
chr213620824136209246E07220195
chr213618867636188995E082630
chr213622915836229253E08241112
chr213622928236229336E08241236