rs2749100

Homo sapiens
G>T
PGM1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0312 (9343/29918,GnomAD)
T=0334 (9726/29118,TOPMED)
T=0334 (1671/5008,1000G)
T=0222 (855/3854,ALSPAC)
T=0221 (819/3708,TWINSUK)
chr1:63659308 (GRCh38.p7) (1p31.3)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.63659308G>T
GRCh37.p13 chr 1NC_000001.10:g.64124979G>T
PGM1 RefSeqGeneNG_016966.1:g.71033G>T

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
1000GenomesAfricanSub1322G=0.515T=0.485
1000GenomesAmericanSub694G=0.610T=0.390
1000GenomesEast AsianSub1008G=0.714T=0.286
1000GenomesEuropeSub1006G=0.726T=0.274
1000GenomesGlobalStudy-wide5008G=0.666T=0.334
1000GenomesSouth AsianSub978G=0.800T=0.200
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.778T=0.222
The Genome Aggregation DatabaseAfricanSub8686G=0.561T=0.439
The Genome Aggregation DatabaseAmericanSub832G=0.630T=0.370
The Genome Aggregation DatabaseEast AsianSub1620G=0.746T=0.254
The Genome Aggregation DatabaseEuropeSub18478G=0.744T=0.255
The Genome Aggregation DatabaseGlobalStudy-wide29918G=0.687T=0.312
The Genome Aggregation DatabaseOtherSub302G=0.720T=0.280
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.666T=0.334
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.779T=0.221
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
rs27491007.63E-07alcohol consumption21665994

eQTL of rs2749100 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 rs2749100 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 )
chr16407837664078513E067-46466
chr16407870464079142E067-45837
chr16408863464089292E067-35687
chr16407837664078513E068-46466
chr16408144864081915E068-43064
chr16408200764082105E068-42874
chr16408863464089292E068-35687
chr16413998664141001E06815007
chr16407837664078513E069-46466
chr16407870464079142E069-45837
chr16408144864081915E069-43064
chr16408200764082105E069-42874
chr16415682364156888E06931844
chr16415713764157261E06932158
chr16416340364163697E06938424
chr16416388464164427E06938905
chr16416515264165382E06940173
chr16410872364108792E070-16187
chr16410890164108951E070-16028
chr16410898364109138E070-15841
chr16411154664111722E070-13257
chr16416887864169157E07043899
chr16416925864169308E07044279
chr16416940064169582E07044421
chr16408144864081915E071-43064
chr16408200764082105E071-42874
chr16408221764082363E071-42616
chr16413998664141001E07115007
chr16416320364163347E07138224
chr16416340364163697E07138424
chr16416515264165382E07140173
chr16408863464089292E072-35687
chr16408960764090320E072-34659
chr16410142864101659E072-23320
chr16410205364102103E072-22876
chr16416061164160818E07235632
chr16416091864161040E07235939
chr16416107764161221E07236098
chr16416320364163347E07238224
chr16416340364163697E07238424
chr16416388464164427E07238905
chr16408144864081915E073-43064
chr16408200764082105E073-42874
chr16408200764082105E074-42874
chr16408221764082363E074-42616
chr16408863464089292E074-35687
chr16409177264091822E074-33157
chr16413998664141001E07415007
chr16408200764082105E081-42874
chr16408221764082363E081-42616
chr16408649964086636E081-38343
chr16408683464087062E081-37917
chr16408715764087315E081-37664
chr16408746164087721E081-37258
chr16408863464089292E081-35687
chr16409075664090893E081-34086
chr16409091464091024E081-33955
chr16410934364110000E081-14979
chr16413998664141001E08115007
chr16414102364142025E08116044
chr16408200764082105E082-42874
chr16408221764082363E082-42616
chr16408649964086636E082-38343
chr16408683464087062E082-37917
chr16408715764087315E082-37664
chr16408746164087721E082-37258
chr16410890164108951E082-16028
chr16410898364109138E082-15841
chr16410934364110000E082-14979
chr16411154664111722E082-13257
chr16414102364142025E08216044
chr16416887864169157E08243899
chr16416925864169308E08244279