rs2269240

Homo sapiens
T>C
PGM1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0217 (6518/29918,GnomAD)
C=0199 (5805/29118,TOPMED)
C=0226 (1130/5008,1000G)
C=0202 (777/3854,ALSPAC)
C=0194 (719/3708,TWINSUK)
chr1:63643593 (GRCh38.p7) (1p31.3)
AD
GWASdb2
1   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.63643593T>C
GRCh37.p13 chr 1NC_000001.10:g.64109264T>C
PGM1 RefSeqGeneNG_016966.1:g.55318T>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=0.815C=0.185
1000GenomesAmericanSub694T=0.600C=0.400
1000GenomesEast AsianSub1008T=0.791C=0.209
1000GenomesEuropeSub1006T=0.765C=0.235
1000GenomesGlobalStudy-wide5008T=0.774C=0.226
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.798C=0.202
The Genome Aggregation DatabaseAfricanSub8716T=0.814C=0.186
The Genome Aggregation DatabaseAmericanSub836T=0.610C=0.390
The Genome Aggregation DatabaseEast AsianSub1614T=0.785C=0.215
The Genome Aggregation DatabaseEuropeSub18450T=0.774C=0.225
The Genome Aggregation DatabaseGlobalStudy-wide29918T=0.782C=0.217
The Genome Aggregation DatabaseOtherSub302T=0.790C=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.800C=0.199
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.806C=0.194
PMID Title Author Journal
21665994Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.Kutalik ZHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs22692408.21E-08alcohol consumption21665994

eQTL of rs2269240 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 rs2269240 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 )
chr16407837664078513E067-30751
chr16407870464079142E067-30122
chr16408863464089292E067-19972
chr16407837664078513E068-30751
chr16408144864081915E068-27349
chr16408200764082105E068-27159
chr16408863464089292E068-19972
chr16413998664141001E06830722
chr16407837664078513E069-30751
chr16407870464079142E069-30122
chr16408144864081915E069-27349
chr16408200764082105E069-27159
chr16415682364156888E06947559
chr16415713764157261E06947873
chr16410872364108792E070-472
chr16410890164108951E070-313
chr16410898364109138E070-126
chr16411154664111722E0702282
chr16408144864081915E071-27349
chr16408200764082105E071-27159
chr16408221764082363E071-26901
chr16413998664141001E07130722
chr16408863464089292E072-19972
chr16408960764090320E072-18944
chr16410142864101659E072-7605
chr16410205364102103E072-7161
chr16408144864081915E073-27349
chr16408200764082105E073-27159
chr16408200764082105E074-27159
chr16408221764082363E074-26901
chr16408863464089292E074-19972
chr16409177264091822E074-17442
chr16413998664141001E07430722
chr16408200764082105E081-27159
chr16408221764082363E081-26901
chr16408649964086636E081-22628
chr16408683464087062E081-22202
chr16408715764087315E081-21949
chr16408746164087721E081-21543
chr16408863464089292E081-19972
chr16409075664090893E081-18371
chr16409091464091024E081-18240
chr16410934364110000E08179
chr16413998664141001E08130722
chr16414102364142025E08131759
chr16408200764082105E082-27159
chr16408221764082363E082-26901
chr16408649964086636E082-22628
chr16408683464087062E082-22202
chr16408715764087315E082-21949
chr16408746164087721E082-21543
chr16410890164108951E082-313
chr16410898364109138E082-126
chr16410934364110000E08279
chr16411154664111722E0822282
chr16414102364142025E08231759