rs157672

Homo sapiens
C>T
SGCD : Intron Variant
LOC105377673 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0028 (849/29950,GnomAD)
T=0031 (916/29118,TOPMED)
T=0052 (262/5008,1000G)
T=0002 (9/3854,ALSPAC)
T=0002 (9/3708,TWINSUK)
chr5:156713071 (GRCh38.p7) (5q33.3)
AD
GWASdb2
1   publication(s)
See rs on genome
63 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.156713071C>T
GRCh37.p13 chr 5NC_000005.9:g.156140082C>T
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

Gene: LOC105377673, uncharacterized LOC105377673(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377673 transcript variant X4XR_001742477.1:n.N/AIntron Variant
LOC105377673 transcript variant X1XR_001742474.1:n.N/AGenic Downstream Transcript Variant
LOC105377673 transcript variant X2XR_001742475.1:n.N/AGenic Downstream Transcript Variant
LOC105377673 transcript variant X3XR_001742476.1:n.N/AGenic Downstream Transcript Variant
LOC105377673 transcript variant X5XR_001742478.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.943T=0.057
1000GenomesAmericanSub694C=0.990T=0.010
1000GenomesEast AsianSub1008C=0.832T=0.168
1000GenomesEuropeSub1006C=0.996T=0.004
1000GenomesGlobalStudy-wide5008C=0.948T=0.052
1000GenomesSouth AsianSub978C=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.998T=0.002
The Genome Aggregation DatabaseAfricanSub8708C=0.941T=0.059
The Genome Aggregation DatabaseAmericanSub838C=0.990T=0.010
The Genome Aggregation DatabaseEast AsianSub1618C=0.824T=0.176
The Genome Aggregation DatabaseEuropeSub18484C=0.997T=0.002
The Genome Aggregation DatabaseGlobalStudy-wide29950C=0.971T=0.028
The Genome Aggregation DatabaseOtherSub302C=1.000T=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.968T=0.031
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.998T=0.002
PMID Title Author Journal

P-Value

SNP ID p-value Traits Study
rs1576721.94E-64alcohol consumptionpha001402
rs1576721.22E-36alcohol consumptionpha001400
rs1576728.17E-11alcohol consumptionpha001398

eQTL of rs157672 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 rs157672 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 )
chr5156112607156112670E067-27412
chr5156112791156112919E067-27163
chr5156113310156113638E067-26444
chr5156113774156114228E067-25854
chr5156114553156114907E067-25175
chr5156140485156140985E067403
chr5156112607156112670E068-27412
chr5156112791156112919E068-27163
chr5156113310156113638E068-26444
chr5156113774156114228E068-25854
chr5156114553156114907E068-25175
chr5156107833156108141E069-31941
chr5156112607156112670E069-27412
chr5156112791156112919E069-27163
chr5156113310156113638E069-26444
chr5156113774156114228E069-25854
chr5156114553156114907E069-25175
chr5156140485156140985E069403
chr5156186154156186561E06946072
chr5156113774156114228E070-25854
chr5156114553156114907E070-25175
chr5156102378156102443E071-37639
chr5156102575156102665E071-37417
chr5156105560156105735E071-34347
chr5156107833156108141E071-31941
chr5156112607156112670E071-27412
chr5156112791156112919E071-27163
chr5156113310156113638E071-26444
chr5156113774156114228E071-25854
chr5156114553156114907E071-25175
chr5156140485156140985E071403
chr5156143650156143832E0713568
chr5156185079156185167E07144997
chr5156185202156185308E07145120
chr5156185461156185663E07145379
chr5156186154156186561E07146072
chr5156107833156108141E072-31941
chr5156108454156108534E072-31548
chr5156112607156112670E072-27412
chr5156112791156112919E072-27163
chr5156113310156113638E072-26444
chr5156113774156114228E072-25854
chr5156114553156114907E072-25175
chr5156140485156140985E072403
chr5156185079156185167E07244997
chr5156185202156185308E07245120
chr5156186154156186561E07246072
chr5156186699156187003E07246617
chr5156113310156113638E073-26444
chr5156113774156114228E073-25854
chr5156105250156105303E074-34779
chr5156107833156108141E074-31941
chr5156112607156112670E074-27412
chr5156112791156112919E074-27163
chr5156113310156113638E074-26444
chr5156113774156114228E074-25854
chr5156114553156114907E074-25175
chr5156140485156140985E074403
chr5156142387156142624E0742305
chr5156142878156142950E0742796
chr5156143650156143832E0743568
chr5156182825156183012E07442743
chr5156186154156186561E07446072