rs2269241

Homo sapiens
T>C
PGM1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0233 (6977/29928,GnomAD)
C=0218 (6358/29118,TOPMED)
C=0245 (1229/5008,1000G)
C=0201 (776/3854,ALSPAC)
C=0194 (719/3708,TWINSUK)
chr1:63643100 (GRCh38.p7) (1p31.3)
AD
GWASdb2
7   publication(s)
See rs on genome
56 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.63643100T>C
GRCh37.p13 chr 1NC_000001.10:g.64108771T>C
PGM1 RefSeqGeneNG_016966.1:g.54825T>C

Gene: PGM1, phosphoglucomutase 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PGM1 transcript variant 2NM_001172818.1:c.N/AIntron Variant
PGM1 transcript variant 3NM_001172819.1:c.N/AIntron Variant
PGM1 transcript variant 1NM_002633.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.741C=0.259
1000GenomesAmericanSub694T=0.600C=0.400
1000GenomesEast AsianSub1008T=0.791C=0.209
1000GenomesEuropeSub1006T=0.765C=0.235
1000GenomesGlobalStudy-wide5008T=0.755C=0.245
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.799C=0.201
The Genome Aggregation DatabaseAfricanSub8716T=0.761C=0.239
The Genome Aggregation DatabaseAmericanSub838T=0.610C=0.390
The Genome Aggregation DatabaseEast AsianSub1616T=0.783C=0.217
The Genome Aggregation DatabaseEuropeSub18456T=0.774C=0.225
The Genome Aggregation DatabaseGlobalStudy-wide29928T=0.766C=0.233
The Genome Aggregation DatabaseOtherSub302T=0.790C=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.781C=0.218
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.806C=0.194
PMID Title Author Journal
20805105Synthetic associations in the context of genome-wide association scan signals.Orozco GHum Mol Genet
26904692Genetic Risk Score Modelling for Disease Progression in New-Onset Type 1 Diabetes Patients: Increased Genetic Load of Islet-Expressed and Cytokine-Regulated Candidate Genes Predicts Poorer Glycemic Control.Brorsson CAJ Diabetes Res
20885991Advances and challenges in biomarker development for type 1 diabetes prediction and prevention using omic technologies.Carey CExpert Opin Med Diagn
21665994Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.Kutalik ZHum Mol Genet
20587799Genetics of type 1 diabetes: what's next?Pociot FDiabetes
19430480Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.Barrett JCNat Genet
19761607Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.Wongseree WBMC Bioinformatics

P-Value

SNP ID p-value Traits Study
rs22692413.57E-08alcohol consumption21665994

eQTL of rs2269241 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 rs2269241 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 )
chr16407837664078513E067-30258
chr16407870464079142E067-29629
chr16408863464089292E067-19479
chr16407837664078513E068-30258
chr16408144864081915E068-26856
chr16408200764082105E068-26666
chr16408863464089292E068-19479
chr16413998664141001E06831215
chr16407837664078513E069-30258
chr16407870464079142E069-29629
chr16408144864081915E069-26856
chr16408200764082105E069-26666
chr16415682364156888E06948052
chr16415713764157261E06948366
chr16410872364108792E0700
chr16410890164108951E070130
chr16410898364109138E070212
chr16411154664111722E0702775
chr16408144864081915E071-26856
chr16408200764082105E071-26666
chr16408221764082363E071-26408
chr16413998664141001E07131215
chr16408863464089292E072-19479
chr16408960764090320E072-18451
chr16410142864101659E072-7112
chr16410205364102103E072-6668
chr16408144864081915E073-26856
chr16408200764082105E073-26666
chr16408200764082105E074-26666
chr16408221764082363E074-26408
chr16408863464089292E074-19479
chr16409177264091822E074-16949
chr16413998664141001E07431215
chr16408200764082105E081-26666
chr16408221764082363E081-26408
chr16408649964086636E081-22135
chr16408683464087062E081-21709
chr16408715764087315E081-21456
chr16408746164087721E081-21050
chr16408863464089292E081-19479
chr16409075664090893E081-17878
chr16409091464091024E081-17747
chr16410934364110000E081572
chr16413998664141001E08131215
chr16414102364142025E08132252
chr16408200764082105E082-26666
chr16408221764082363E082-26408
chr16408649964086636E082-22135
chr16408683464087062E082-21709
chr16408715764087315E082-21456
chr16408746164087721E082-21050
chr16410890164108951E082130
chr16410898364109138E082212
chr16410934364110000E082572
chr16411154664111722E0822775
chr16414102364142025E08232252