rs17178655

Homo sapiens
C>T
MSMB : Intron Variant
LOC105378287 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0203 (6083/29942,GnomAD)
A=0187 (5454/29118,TOPMED)
A=0222 (1113/5008,1000G)
A=0228 (879/3854,ALSPAC)
A=0226 (838/3708,TWINSUK)
chr10:46034023 (GRCh38.p7) (10q11.22)
ND
GWASdb2
5   publication(s)
See rs on genome
92 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.46034023C>T
GRCh37.p13 chr 10 fix patch HG1211_PATCHNW_003871068.1:g.305138C>T
NCOA4 RefSeqGeneNG_023372.1:g.1692G>A
MSMB RefSeqGeneNG_011551.1:g.17247G>A
GRCh37.p13 chr 10NC_000010.10:g.51561799G>A

Gene: MSMB, microseminoprotein, beta-(minus strand)

Molecule type Change Amino acid[Codon] SO Term
MSMB transcript variant PSP94NM_002443.3:c.N/AIntron Variant
MSMB transcript variant PSP57NM_138634.2:c.N/AIntron Variant

Gene: LOC105378287, uncharacterized LOC105378287(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378287 transcriptXR_945923.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.832T=0.168
1000GenomesAmericanSub694C=0.810T=0.190
1000GenomesEast AsianSub1008C=0.696T=0.304
1000GenomesEuropeSub1006C=0.769T=0.231
1000GenomesGlobalStudy-wide5008C=0.778T=0.222
1000GenomesSouth AsianSub978C=0.770T=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.772T=0.228
The Genome Aggregation DatabaseAfricanSub8702C=0.821T=0.179
The Genome Aggregation DatabaseAmericanSub836C=0.840T=0.160
The Genome Aggregation DatabaseEast AsianSub1612C=0.736T=0.264
The Genome Aggregation DatabaseEuropeSub18490C=0.789T=0.210
The Genome Aggregation DatabaseGlobalStudy-wide29942C=0.796T=0.203
The Genome Aggregation DatabaseOtherSub302C=0.780T=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.812T=0.187
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.774T=0.226
PMID Title Author Journal
20696662Polymorphisms at the Microseminoprotein-beta locus associated with physiologic variation in beta-microseminoprotein and prostate-specific antigen levels.Xu XCancer Epidemiol Biomarkers Prev
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet
22101116Evaluation of multiple risk-associated single nucleotide polymorphisms versus prostate-specific antigen at baseline to predict prostate cancer in unscreened men.Klein RJEur Urol
19383797Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility.Lou HProc Natl Acad Sci U S A
26068399An analysis of the association between prostate cancer risk loci, PSA levels, disease aggressiveness and disease-specific mortality.Sullivan JBr J Cancer

P-Value

SNP ID p-value Traits Study
rs171786557.78E-06alcohol and nictotine co-dependence20158304

eQTL of rs17178655 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:51561799FAM21AENSG00000099290.11G>A2.3247e-21-265849Cerebellar_Hemisphere

meQTL of rs17178655 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 )
chr10290440290490E067-14648
chr10290985291116E067-14022
chr10321004321089E06715866
chr10338932338982E06733794
chr10339171339221E06734033
chr10339288339338E06734150
chr10339542339638E06734404
chr10340144340306E06735006
chr10343106343831E06737968
chr10343924344003E06738786
chr10344049344318E06738911
chr10338932338982E06833794
chr10339171339221E06834033
chr10339288339338E06834150
chr10339542339638E06834404
chr10340144340306E06835006
chr10343106343831E06837968
chr10343924344003E06838786
chr10344049344318E06838911
chr10344403344453E06839265
chr10344740344858E06839602
chr10287477287640E069-17498
chr10290440290490E069-14648
chr10321004321089E06915866
chr10338932338982E06933794
chr10339171339221E06934033
chr10339288339338E06934150
chr10339542339638E06934404
chr10340144340306E06935006
chr10343106343831E06937968
chr10343924344003E06938786
chr10344049344318E06938911
chr10287923288291E070-16847
chr10288443288559E070-16579
chr10321004321089E07015866
chr10287477287640E071-17498
chr10321004321089E07115866
chr10335847336053E07130709
chr10336089336191E07130951
chr10336373336438E07131235
chr10336950336990E07131812
chr10338932338982E07133794
chr10339171339221E07134033
chr10339288339338E07134150
chr10339542339638E07134404
chr10340144340306E07135006
chr10343106343831E07137968
chr10343924344003E07138786
chr10344049344318E07138911
chr10344403344453E07139265
chr10287477287640E072-17498
chr10290440290490E072-14648
chr10321004321089E07215866
chr10328668328794E07223530
chr10338932338982E07233794
chr10339171339221E07234033
chr10339288339338E07234150
chr10339542339638E07234404
chr10340144340306E07235006
chr10343106343831E07237968
chr10343924344003E07238786
chr10344049344318E07238911
chr10344403344453E07239265
chr10339542339638E07334404
chr10340144340306E07335006
chr10343106343831E07337968
chr10287477287640E074-17498
chr10287923288291E074-16847
chr10290440290490E074-14648
chr10317286317666E07412148
chr10321004321089E07415866
chr10335847336053E07430709
chr10336089336191E07430951
chr10336373336438E07431235
chr10338932338982E07433794
chr10339171339221E07434033
chr10339288339338E07434150
chr10339542339638E07434404
chr10340144340306E07435006
chr10343106343831E07437968
chr10343924344003E07438786
chr10344049344318E07438911
chr10344403344453E07439265
chr10344740344858E07439602
chr10287477287640E081-17498
chr10291259291444E081-13694
chr10291506291586E081-13552
chr10291655291723E081-13415
chr10291842292190E081-12948
chr10352079352249E08246941
chr10352252352502E08247114
chr10352608353131E08247470