rs10515739

Homo sapiens
T>C
SGCD : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0024 (731/29976,GnomAD)
C=0021 (638/29118,TOPMED)
C=0051 (257/5008,1000G)
C=0002 (7/3854,ALSPAC)
C=0001 (5/3708,TWINSUK)
chr5:156590621 (GRCh38.p7) (5q33.3)
AD
GWASdb2
1   publication(s)
See rs on genome
117 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.156590621T>C
GRCh37.p13 chr 5NC_000005.9:g.156017631T>C
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
1000GenomesAfricanSub1322T=0.956C=0.044
1000GenomesAmericanSub694T=0.990C=0.010
1000GenomesEast AsianSub1008T=0.817C=0.183
1000GenomesEuropeSub1006T=0.998C=0.002
1000GenomesGlobalStudy-wide5008T=0.949C=0.051
1000GenomesSouth AsianSub978T=0.990C=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.998C=0.002
The Genome Aggregation DatabaseAfricanSub8728T=0.955C=0.045
The Genome Aggregation DatabaseAmericanSub838T=0.980C=0.020
The Genome Aggregation DatabaseEast AsianSub1612T=0.823C=0.177
The Genome Aggregation DatabaseEuropeSub18496T=0.998C=0.001
The Genome Aggregation DatabaseGlobalStudy-wide29976T=0.975C=0.024
The Genome Aggregation DatabaseOtherSub302T=1.000C=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.978C=0.021
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.999C=0.001
PMID Title Author Journal

P-Value

SNP ID p-value Traits Study
rs105157391.83E-59alcohol consumptionpha001402
rs105157397.15E-41alcohol consumptionpha001400
rs105157392.65E-10alcohol consumptionpha001398

eQTL of rs10515739 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 rs10515739 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 )
chr5155984141155984446E067-33185
chr5156009212156009407E067-8224
chr5156009518156009583E067-8048
chr5156011319156011639E067-5992
chr5156011651156012061E067-5570
chr5156012073156012199E067-5432
chr5156012525156012619E067-5012
chr5156012723156012818E067-4813
chr5156013695156013862E067-3769
chr5156014194156014267E067-3364
chr5156015144156015335E067-2296
chr5156015383156016032E067-1599
chr5156016149156016435E067-1196
chr5156016439156016881E067-750
chr5156018022156018965E067391
chr5156022296156022376E0674665
chr5156022452156022824E0674821
chr5156022977156023092E0675346
chr5156050488156050627E06732857
chr5156050775156050832E06733144
chr5155984141155984446E068-33185
chr5156009212156009407E068-8224
chr5156009518156009583E068-8048
chr5156012073156012199E068-5432
chr5156012525156012619E068-5012
chr5156012723156012818E068-4813
chr5156013695156013862E068-3769
chr5156014194156014267E068-3364
chr5156015383156016032E068-1599
chr5156016149156016435E068-1196
chr5156018022156018965E068391
chr5156050488156050627E06832857
chr5156050775156050832E06833144
chr5155984141155984446E069-33185
chr5156011319156011639E069-5992
chr5156011651156012061E069-5570
chr5156012073156012199E069-5432
chr5156012525156012619E069-5012
chr5156012723156012818E069-4813
chr5156013695156013862E069-3769
chr5156014194156014267E069-3364
chr5156015144156015335E069-2296
chr5156015383156016032E069-1599
chr5156016149156016435E069-1196
chr5156016439156016881E069-750
chr5156018022156018965E069391
chr5156022452156022824E0694821
chr5156022977156023092E0695346
chr5156050488156050627E06932857
chr5156050775156050832E06933144
chr5155987015155987362E070-30269
chr5155984141155984446E071-33185
chr5156009212156009407E071-8224
chr5156009518156009583E071-8048
chr5156011319156011639E071-5992
chr5156011651156012061E071-5570
chr5156012073156012199E071-5432
chr5156012525156012619E071-5012
chr5156012723156012818E071-4813
chr5156013695156013862E071-3769
chr5156014194156014267E071-3364
chr5156015383156016032E071-1599
chr5156016149156016435E071-1196
chr5156016439156016881E071-750
chr5156018022156018965E071391
chr5156022296156022376E0714665
chr5156022452156022824E0714821
chr5156026001156026271E0718370
chr5156050775156050832E07133144
chr5156009518156009583E072-8048
chr5156011651156012061E072-5570
chr5156012073156012199E072-5432
chr5156012525156012619E072-5012
chr5156012723156012818E072-4813
chr5156013695156013862E072-3769
chr5156014194156014267E072-3364
chr5156015144156015335E072-2296
chr5156015383156016032E072-1599
chr5156016149156016435E072-1196
chr5156016439156016881E072-750
chr5156018022156018965E072391
chr5156026001156026271E0728370
chr5156050488156050627E07232857
chr5156050775156050832E07233144
chr5155984141155984446E073-33185
chr5156011319156011639E073-5992
chr5156011651156012061E073-5570
chr5156012073156012199E073-5432
chr5156012525156012619E073-5012
chr5156012723156012818E073-4813
chr5156014194156014267E073-3364
chr5156016439156016881E073-750
chr5156018022156018965E073391
chr5155984141155984446E074-33185
chr5155998621155998673E074-18958
chr5156009212156009407E074-8224
chr5156009518156009583E074-8048
chr5156011319156011639E074-5992
chr5156011651156012061E074-5570
chr5156012073156012199E074-5432
chr5156012525156012619E074-5012
chr5156012723156012818E074-4813
chr5156013695156013862E074-3769
chr5156014194156014267E074-3364
chr5156015144156015335E074-2296
chr5156015383156016032E074-1599
chr5156016149156016435E074-1196
chr5156016439156016881E074-750
chr5156018022156018965E074391
chr5156019686156019744E0742055
chr5156022296156022376E0744665
chr5156022452156022824E0744821
chr5156022977156023092E0745346
chr5156050488156050627E07432857
chr5156050775156050832E07433144
chr5156014194156014267E081-3364
chr5155984141155984446E082-33185