rs12490148

Homo sapiens
C>T
SRPRB : Intron Variant
LOC105374116 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0288 (8642/29946,GnomAD)
T=0272 (7930/29118,TOPMED)
T=0322 (1615/5008,1000G)
T=0332 (1280/3854,ALSPAC)
T=0334 (1238/3708,TWINSUK)
chr3:133805129 (GRCh38.p7) (3q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
84 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.133805129C>T
GRCh37.p13 chr 3NC_000003.11:g.133523973C>T

Gene: SRPRB, SRP receptor beta subunit(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SRPRB transcriptNM_021203.3:c.N/AIntron Variant

Gene: LOC105374116, uncharacterized LOC105374116(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374116 transcript variant X1XR_924512.2:n.575G>AG>ANon Coding Transcript Variant
LOC105374116 transcript variant X2XR_924513.2:n.575G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.879T=0.121
1000GenomesAmericanSub694C=0.600T=0.400
1000GenomesEast AsianSub1008C=0.535T=0.465
1000GenomesEuropeSub1006C=0.657T=0.343
1000GenomesGlobalStudy-wide5008C=0.678T=0.322
1000GenomesSouth AsianSub978C=0.630T=0.370
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.668T=0.332
The Genome Aggregation DatabaseAfricanSub8724C=0.827T=0.173
The Genome Aggregation DatabaseAmericanSub838C=0.520T=0.480
The Genome Aggregation DatabaseEast AsianSub1610C=0.559T=0.441
The Genome Aggregation DatabaseEuropeSub18472C=0.677T=0.322
The Genome Aggregation DatabaseGlobalStudy-wide29946C=0.711T=0.288
The Genome Aggregation DatabaseOtherSub302C=0.760T=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.727T=0.272
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.666T=0.334
PMID Title Author Journal
21665994Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.Kutalik ZHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs124901481.98E-12alcohol consumption21665994

eQTL of rs12490148 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 rs12490148 in Fetal Brain

Probe ID Position Gene beta p-value
cg16414030chr3:133502952-0.1266462018250931.7849e-52
cg01448562chr3:133502909-0.08118586194547181.3683e-50
cg08048268chr3:133502702-0.1782667225972031.7736e-44
cg16275903chr3:133524006SRPRB0.07753811709468186.2582e-39
cg11941060chr3:133502564-0.08834008666854851.0120e-31
cg08439880chr3:133502540-0.09527889573198113.9519e-31
cg20276088chr3:133502917-0.04681108837953471.5556e-29

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 )
chr3133482923133483028E067-40945
chr3133483054133483594E067-40379
chr3133483998133484070E067-39903
chr3133562885133562960E06738912
chr3133573215133573347E06749242
chr3133482562133482616E068-41357
chr3133482923133483028E068-40945
chr3133483054133483594E068-40379
chr3133572273133572376E06848300
chr3133572430133572579E06848457
chr3133572588133572638E06848615
chr3133573215133573347E06849242
chr3133476260133476458E069-47515
chr3133482562133482616E069-41357
chr3133482923133483028E069-40945
chr3133483054133483594E069-40379
chr3133483998133484070E069-39903
chr3133484337133484387E069-39586
chr3133540603133541021E06916630
chr3133541191133541245E06917218
chr3133572273133572376E06948300
chr3133572430133572579E06948457
chr3133572588133572638E06948615
chr3133573215133573347E06949242
chr3133482923133483028E070-40945
chr3133483054133483594E070-40379
chr3133547093133547193E07023120
chr3133547516133547745E07023543
chr3133547924133548172E07023951
chr3133572273133572376E07048300
chr3133572430133572579E07048457
chr3133572588133572638E07048615
chr3133573215133573347E07049242
chr3133482562133482616E071-41357
chr3133482923133483028E071-40945
chr3133483054133483594E071-40379
chr3133483998133484070E071-39903
chr3133484337133484387E071-39586
chr3133540337133540417E07116364
chr3133572273133572376E07148300
chr3133572430133572579E07148457
chr3133572588133572638E07148615
chr3133573215133573347E07149242
chr3133482923133483028E072-40945
chr3133483054133483594E072-40379
chr3133483998133484070E072-39903
chr3133484337133484387E072-39586
chr3133573215133573347E07249242
chr3133482923133483028E073-40945
chr3133483054133483594E073-40379
chr3133540006133540074E07316033
chr3133540337133540417E07316364
chr3133540603133541021E07316630
chr3133541035133541081E07317062
chr3133541191133541245E07317218
chr3133572273133572376E07348300
chr3133573215133573347E07349242
chr3133476260133476458E074-47515
chr3133482562133482616E074-41357
chr3133482923133483028E074-40945
chr3133483054133483594E074-40379
chr3133483998133484070E074-39903
chr3133484337133484387E074-39586
chr3133540006133540074E07416033
chr3133540337133540417E07416364
chr3133540603133541021E07416630
chr3133541035133541081E07417062
chr3133541191133541245E07417218
chr3133541431133541497E07417458
chr3133541623133541762E07417650
chr3133541910133541964E07417937
chr3133572430133572579E07448457
chr3133572588133572638E07448615
chr3133573215133573347E07449242
chr3133526132133526214E0812159
chr3133572273133572376E08148300
chr3133573215133573347E08149242
chr3133547516133547745E08223543
chr3133547924133548172E08223951
chr3133548284133548391E08224311
chr3133572273133572376E08248300
chr3133572430133572579E08248457
chr3133572588133572638E08248615
chr3133573215133573347E08249242










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3133524082133525550E067109
chr3133525588133525634E0671615
chr3133524082133525550E068109
chr3133525588133525634E0681615
chr3133524082133525550E069109
chr3133524082133525550E070109
chr3133525588133525634E0701615
chr3133524082133525550E071109
chr3133525588133525634E0711615
chr3133524082133525550E072109
chr3133525588133525634E0721615
chr3133524082133525550E073109
chr3133525588133525634E0731615
chr3133524082133525550E074109
chr3133525588133525634E0741615
chr3133524082133525550E081109
chr3133525588133525634E0811615
chr3133524082133525550E082109
chr3133525588133525634E0821615