rs10117516

Homo sapiens
C>G / C>T
FREM1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0443 (13256/29874,GnomAD)
T=0462 (13455/29118,TOPMED)
T=0423 (2117/5008,1000G)
T=0425 (1638/3854,ALSPAC)
T=0434 (1608/3708,TWINSUK)
chr9:14749436 (GRCh38.p7) (9p22.3)
AD
GWASdb2
1   publication(s)
See rs on genome
45 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.14749436C>G
GRCh38.p7 chr 9NC_000009.12:g.14749436C>T
GRCh37.p13 chr 9NC_000009.11:g.14749434C>G
GRCh37.p13 chr 9NC_000009.11:g.14749434C>T
FREM1 RefSeqGeneNG_017005.2:g.165801G>C
FREM1 RefSeqGeneNG_017005.2:g.165801G>A

Gene: FREM1, FRAS1 related extracellular matrix 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
FREM1 transcript variant 2NM_001177704.1:c.N/AIntron Variant
FREM1 transcript variant 1NM_144966.5:c.N/AIntron Variant
FREM1 transcript variant X9XM_005251382.3:c.N/AIntron Variant
FREM1 transcript variant X22XM_005251384.4:c.N/AIntron Variant
FREM1 transcript variant X21XM_006716729.3:c.N/AIntron Variant
FREM1 transcript variant X20XM_011517758.2:c.N/AIntron Variant
FREM1 transcript variant X1XM_017014316.1:c.N/AIntron Variant
FREM1 transcript variant X2XM_017014317.1:c.N/AIntron Variant
FREM1 transcript variant X3XM_017014318.1:c.N/AIntron Variant
FREM1 transcript variant X4XM_017014319.1:c.N/AIntron Variant
FREM1 transcript variant X5XM_017014320.1:c.N/AIntron Variant
FREM1 transcript variant X6XM_017014321.1:c.N/AIntron Variant
FREM1 transcript variant X6XM_017014322.1:c.N/AIntron Variant
FREM1 transcript variant X7XM_017014323.1:c.N/AIntron Variant
FREM1 transcript variant X10XM_017014324.1:c.N/AIntron Variant
FREM1 transcript variant X11XM_017014325.1:c.N/AIntron Variant
FREM1 transcript variant X11XM_017014326.1:c.N/AIntron Variant
FREM1 transcript variant X13XM_017014327.1:c.N/AIntron Variant
FREM1 transcript variant X14XM_017014328.1:c.N/AGenic Downstream Transcript Variant
FREM1 transcript variant X15XM_017014329.1:c.N/AGenic Downstream Transcript Variant
FREM1 transcript variant X20XM_017014330.1:c.N/AGenic Downstream Transcript Variant
FREM1 transcript variant X16XR_001746194.1:n.N/AIntron Variant
FREM1 transcript variant X17XR_001746195.1:n.N/AIntron Variant
FREM1 transcript variant X18XR_001746196.1:n.N/AGenic Downstream Transcript Variant
FREM1 transcript variant X19XR_001746197.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.446T=0.554
1000GenomesAmericanSub694C=0.600T=0.400
1000GenomesEast AsianSub1008C=0.731T=0.269
1000GenomesEuropeSub1006C=0.597T=0.403
1000GenomesGlobalStudy-wide5008C=0.577T=0.423
1000GenomesSouth AsianSub978C=0.560T=0.440
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.575T=0.425
The Genome Aggregation DatabaseAfricanSub8678C=0.479T=0.521
The Genome Aggregation DatabaseAmericanSub838C=0.620T=0.38,
The Genome Aggregation DatabaseEast AsianSub1618C=0.739T=0.261
The Genome Aggregation DatabaseEuropeSub18440C=0.571T=0.428
The Genome Aggregation DatabaseGlobalStudy-wide29874C=0.556T=0.443
The Genome Aggregation DatabaseOtherSub300C=0.700T=0.30,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.537T=0.462
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.566T=0.434
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs101175160.000137alcohol dependence24277619
rs101175160.000261alcohol consumption (maxi-drinks)24277619

eQTL of rs10117516 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 rs10117516 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 )
chr97265746672658081E067-15468
chr97263580472636687E068-36862
chr97263707772637226E068-36323
chr97263737072637420E068-36129
chr97266384372663916E068-9633
chr97269525572696484E06821706
chr97265167172651870E069-21679
chr97266417672665067E069-8482
chr97262842072629141E070-44408
chr97263520072635501E070-38048
chr97263550872635775E070-37774
chr97263580472636687E070-36862
chr97263707772637226E070-36323
chr97263737072637420E070-36129
chr97265746672658081E070-15468
chr97266417672665067E070-8482
chr97266855172669410E070-4139
chr97269397772695161E07020428
chr97270659572706808E07033046
chr97270685272706938E07033303
chr97270700172707108E07033452
chr97270721372707455E07033664
chr97263580472636687E071-36862
chr97263707772637226E071-36323
chr97265106972651149E071-22400
chr97265167172651870E071-21679
chr97265746672658081E071-15468
chr97266358172663824E071-9725
chr97266384372663916E071-9633
chr97266417672665067E071-8482
chr97266384372663916E072-9633
chr97266358172663824E073-9725
chr97266384372663916E073-9633
chr97266417672665067E073-8482
chr97269044872690488E07316899
chr97269054172690591E07316992
chr97263580472636687E074-36862
chr97265167172651870E074-21679
chr97265188772652110E074-21439
chr97269525572696484E07421706
chr97269397772695161E08120428
chr97270659572706808E08233046
chr97270685272706938E08233303
chr97270700172707108E08233452
chr97270721372707455E08233664










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr97265820372659330E067-14219
chr97265934372660215E067-13334
chr97265820372659330E068-14219
chr97265934372660215E068-13334
chr97265820372659330E069-14219
chr97265934372660215E069-13334
chr97265934372660215E070-13334
chr97265820372659330E071-14219
chr97265934372660215E071-13334
chr97265820372659330E072-14219
chr97265934372660215E072-13334
chr97265820372659330E073-14219
chr97265934372660215E073-13334
chr97265820372659330E074-14219
chr97265934372660215E074-13334
chr97265934372660215E082-13334