rs2049675

Homo sapiens
C>T
LOC105371822 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0206 (6153/29854,GnomAD)
T=0174 (5080/29118,TOPMED)
T=0220 (1101/5008,1000G)
T=0228 (877/3854,ALSPAC)
T=0220 (814/3708,TWINSUK)
chr17:50257586 (GRCh38.p7) (17q21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
34 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.50257586C>T
GRCh37.p13 chr 17NC_000017.10:g.48334947C>T

Gene: LOC105371822, uncharacterized LOC105371822(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105371822 transcript variant X5XR_001752937.1:n....XR_001752937.1:n.958C>TC>TNon Coding Transcript Variant
LOC105371822 transcript variant X7XR_001752939.1:n....XR_001752939.1:n.958C>TC>TNon Coding Transcript Variant
LOC105371822 transcript variant X1XR_001752933.1:n.N/AIntron Variant
LOC105371822 transcript variant X2XR_001752934.1:n.N/AGenic Upstream Transcript Variant
LOC105371822 transcript variant X3XR_001752935.1:n.N/AGenic Upstream Transcript Variant
LOC105371822 transcript variant X4XR_001752936.1:n.N/AGenic Upstream Transcript Variant
LOC105371822 transcript variant X6XR_001752938.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.897T=0.103
1000GenomesAmericanSub694C=0.780T=0.220
1000GenomesEast AsianSub1008C=0.731T=0.269
1000GenomesEuropeSub1006C=0.805T=0.195
1000GenomesGlobalStudy-wide5008C=0.780T=0.220
1000GenomesSouth AsianSub978C=0.640T=0.360
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.772T=0.228
The Genome Aggregation DatabaseAfricanSub8682C=0.870T=0.130
The Genome Aggregation DatabaseAmericanSub838C=0.810T=0.190
The Genome Aggregation DatabaseEast AsianSub1620C=0.731T=0.269
The Genome Aggregation DatabaseEuropeSub18412C=0.763T=0.237
The Genome Aggregation DatabaseGlobalStudy-wide29854C=0.793T=0.206
The Genome Aggregation DatabaseOtherSub302C=0.800T=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.825T=0.174
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.780T=0.220
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs20496750.00096alcohol dependence20201924

eQTL of rs2049675 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 rs2049675 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 )
chr174838204648382135E06747099
chr174838217148382457E06747224
chr174834742648348766E06812479
chr174836655148366658E06831604
chr174836670248366936E06831755
chr174836705848368182E06832111
chr174838217148382457E06847224
chr174834742648348766E06912479
chr174834455848345929E0709611
chr174834294648344548E0717999
chr174834742648348766E07112479
chr174836578648366043E07130839
chr174836609248366197E07131145
chr174836622748366297E07131280
chr174836655148366658E07131604
chr174836670248366936E07131755
chr174836705848368182E07132111
chr174838217148382457E07147224
chr174834742648348766E07212479
chr174836655148366658E07231604
chr174836670248366936E07231755
chr174838217148382457E07347224
chr174834742648348766E07412479
chr174836670248366936E07431755
chr174836705848368182E07432111
chr174828495548285150E081-49797
chr174833600548337839E0811058
chr174833787448338244E0812927
chr174833829748338404E0813350
chr174834294648344548E0817999
chr174834455848345929E0819611
chr174834948348349561E08114536
chr174831503248315312E082-19635
chr174834455848345929E0829611