rs17053572

Homo sapiens
A>G
SGCD : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0035 (1055/29968,GnomAD)
G=0029 (861/29118,TOPMED)
G=0043 (213/5008,1000G)
G=0032 (123/3854,ALSPAC)
G=0039 (146/3708,TWINSUK)
chr5:156467487 (GRCh38.p7) (5q33.3)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.156467487A>G
GRCh37.p13 chr 5NC_000005.9:g.155894497A>G
SGCD RefSeqGene LRG_205

Gene: SGCD, sarcoglycan delta(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SGCD transcript variant 1NM_000337.5:c.N/AIntron Variant
SGCD transcript variant 3NM_001128209.1:c.N/AIntron Variant
SGCD transcript variant 2NM_172244.2:c.N/AIntron Variant
SGCD transcript variant X3XM_005265966.4:c.N/AIntron Variant
SGCD transcript variant X5XM_005265967.2:c.N/AIntron Variant
SGCD transcript variant X4XM_011534621.2:c.N/AIntron Variant
SGCD transcript variant X1XM_017009723.1:c.N/AIntron Variant
SGCD transcript variant X2XM_017009724.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.992G=0.008
1000GenomesAmericanSub694A=0.930G=0.070
1000GenomesEast AsianSub1008A=0.973G=0.027
1000GenomesEuropeSub1006A=0.952G=0.048
1000GenomesGlobalStudy-wide5008A=0.957G=0.043
1000GenomesSouth AsianSub978A=0.920G=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.968G=0.032
The Genome Aggregation DatabaseAfricanSub8734A=0.989G=0.011
The Genome Aggregation DatabaseAmericanSub838A=0.940G=0.060
The Genome Aggregation DatabaseEast AsianSub1606A=0.974G=0.026
The Genome Aggregation DatabaseEuropeSub18490A=0.953G=0.046
The Genome Aggregation DatabaseGlobalStudy-wide29968A=0.964G=0.035
The Genome Aggregation DatabaseOtherSub300A=0.970G=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.970G=0.029
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.961G=0.039
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs170535720.000507nicotine smoking19268276

eQTL of rs17053572 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 rs17053572 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 )
chr5155861324155862359E067-32138
chr5155887030155887133E067-7364
chr5155887173155887299E067-7198
chr5155901067155901210E0676570
chr5155901274155901710E0676777
chr5155901781155901886E0677284
chr5155902055155902109E0677558
chr5155902330155902438E0677833
chr5155902530155903241E0678033
chr5155903248155903402E0678751
chr5155903627155903841E0679130
chr5155903866155904512E0679369
chr5155904537155904630E06710040
chr5155924051155924155E06729554
chr5155924235155924320E06729738
chr5155924364155924576E06729867
chr5155924758155925235E06730261
chr5155900633155900958E0686136
chr5155901781155901886E0687284
chr5155902055155902109E0687558
chr5155902330155902438E0687833
chr5155902530155903241E0688033
chr5155903248155903402E0688751
chr5155903627155903841E0689130
chr5155903866155904512E0689369
chr5155904537155904630E06810040
chr5155906619155907263E06812122
chr5155924051155924155E06829554
chr5155924235155924320E06829738
chr5155924364155924576E06829867
chr5155924758155925235E06830261
chr5155925317155925441E06830820
chr5155925484155925576E06830987
chr5155861324155862359E069-32138
chr5155870414155870494E069-24003
chr5155873230155873344E069-21153
chr5155896654155897123E0692157
chr5155900122155900618E0695625
chr5155900633155900958E0696136
chr5155901067155901210E0696570
chr5155901274155901710E0696777
chr5155901781155901886E0697284
chr5155902055155902109E0697558
chr5155902330155902438E0697833
chr5155902530155903241E0698033
chr5155903248155903402E0698751
chr5155903627155903841E0699130
chr5155903866155904512E0699369
chr5155904537155904630E06910040
chr5155923173155924030E06928676
chr5155861324155862359E070-32138
chr5155864411155864763E070-29734
chr5155865207155865406E070-29091
chr5155900122155900618E0705625
chr5155900633155900958E0706136
chr5155901067155901210E0706570
chr5155901781155901886E0707284
chr5155902055155902109E0707558
chr5155902330155902438E0707833
chr5155902530155903241E0708033
chr5155903248155903402E0708751
chr5155903627155903841E0709130
chr5155903866155904512E0709369
chr5155905350155905430E07010853
chr5155924758155925235E07030261
chr5155896654155897123E0712157
chr5155900122155900618E0715625
chr5155900633155900958E0716136
chr5155902055155902109E0717558
chr5155902330155902438E0717833
chr5155902530155903241E0718033
chr5155903248155903402E0718751
chr5155903627155903841E0719130
chr5155903866155904512E0719369
chr5155904537155904630E07110040
chr5155904796155904892E07110299
chr5155923173155924030E07128676
chr5155924051155924155E07129554
chr5155924235155924320E07129738
chr5155924364155924576E07129867
chr5155925317155925441E07130820
chr5155925484155925576E07130987
chr5155925665155925873E07131168
chr5155925895155926085E07131398
chr5155861324155862359E072-32138
chr5155870414155870494E072-24003
chr5155896654155897123E0722157
chr5155900122155900618E0725625
chr5155900633155900958E0726136
chr5155902055155902109E0727558
chr5155902330155902438E0727833
chr5155902530155903241E0728033
chr5155903248155903402E0728751
chr5155903627155903841E0729130
chr5155903866155904512E0729369
chr5155904537155904630E07210040
chr5155905350155905430E07210853
chr5155923173155924030E07228676
chr5155924051155924155E07229554
chr5155924235155924320E07229738
chr5155924364155924576E07229867
chr5155925317155925441E07230820
chr5155925484155925576E07230987
chr5155925665155925873E07231168
chr5155925895155926085E07231398
chr5155870414155870494E073-24003
chr5155900633155900958E0736136
chr5155901067155901210E0736570
chr5155901781155901886E0737284
chr5155902055155902109E0737558
chr5155902330155902438E0737833
chr5155902530155903241E0738033
chr5155903248155903402E0738751
chr5155903627155903841E0739130
chr5155923173155924030E07328676
chr5155896654155897123E0742157
chr5155900633155900958E0746136
chr5155901067155901210E0746570
chr5155901274155901710E0746777
chr5155901781155901886E0747284
chr5155902055155902109E0747558
chr5155902330155902438E0747833
chr5155902530155903241E0748033
chr5155903248155903402E0748751
chr5155903627155903841E0749130
chr5155903866155904512E0749369
chr5155904537155904630E07410040
chr5155904796155904892E07410299
chr5155905350155905430E07410853
chr5155909995155910154E07415498
chr5155910267155910430E07415770
chr5155923173155924030E07428676
chr5155924051155924155E07429554
chr5155924235155924320E07429738
chr5155924364155924576E07429867
chr5155925317155925441E07430820
chr5155925484155925576E07430987
chr5155925665155925873E07431168
chr5155925895155926085E07431398
chr5155846788155846892E081-47605
chr5155900122155900618E0815625
chr5155900633155900958E0816136
chr5155901067155901210E0816570
chr5155901274155901710E0816777
chr5155901781155901886E0817284
chr5155902055155902109E0817558
chr5155902330155902438E0817833
chr5155902530155903241E0818033
chr5155903248155903402E0818751
chr5155903627155903841E0819130
chr5155924758155925235E08130261
chr5155925317155925441E08130820
chr5155925484155925576E08130987
chr5155925665155925873E08131168
chr5155925895155926085E08131398
chr5155900633155900958E0826136
chr5155901067155901210E0826570
chr5155901274155901710E0826777
chr5155901781155901886E0827284
chr5155902055155902109E0827558
chr5155902330155902438E0827833
chr5155902530155903241E0828033