rs10519663

Homo sapiens
A>C
LOC105370743 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0098 (2951/29988,GnomAD)
C=0101 (2956/29118,TOPMED)
C=0138 (693/5008,1000G)
C=0107 (412/3854,ALSPAC)
C=0111 (411/3708,TWINSUK)
chr15:29687136 (GRCh38.p7) (15q13.1)
ND
GWASdb2
1   publication(s)
See rs on genome
71 Enhancers around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.29687136A>C
GRCh37.p13 chr 15NC_000015.9:g.29979340A>C
GRCh38.p7 chr 15 fix patch HG2139_PATCHNW_011332701.1:g.1858778A>C
GRCh38.p7 chr 15 alt locus HSCHR15_4_CTG8NT_187660.1:g.1971262A>C

Gene: LOC105370743, uncharacterized LOC105370743(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105370743 transcript variant X1XR_932029.2:n.N/AUpstream Transcript Variant
LOC105370743 transcript variant X2XR_932031.2:n.N/AUpstream Transcript Variant
LOC105370743 transcript variant X3XR_932032.2:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.942C=0.058
1000GenomesAmericanSub694A=0.820C=0.180
1000GenomesEast AsianSub1008A=0.878C=0.122
1000GenomesEuropeSub1006A=0.873C=0.127
1000GenomesGlobalStudy-wide5008A=0.862C=0.138
1000GenomesSouth AsianSub978A=0.760C=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.893C=0.107
The Genome Aggregation DatabaseAfricanSub8732A=0.925C=0.075
The Genome Aggregation DatabaseAmericanSub838A=0.850C=0.150
The Genome Aggregation DatabaseEast AsianSub1616A=0.851C=0.149
The Genome Aggregation DatabaseEuropeSub18500A=0.897C=0.102
The Genome Aggregation DatabaseGlobalStudy-wide29988A=0.901C=0.098
The Genome Aggregation DatabaseOtherSub302A=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.898C=0.101
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.889C=0.111
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs105196632.25E-05alcohol and nictotine co-dependence20158304

eQTL of rs10519663 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 rs10519663 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 )
chr152992958129929724E067-49616
chr152992983629929880E067-49460
chr152992989029929972E067-49368
chr152996964929969711E067-9629
chr152996983529969879E067-9461
chr152997008329970168E067-9172
chr152999045129990987E06711111
chr152992958129929724E068-49616
chr152992983629929880E068-49460
chr152992989029929972E068-49368
chr152993024729930530E068-48810
chr152993059929930679E068-48661
chr152996278629964124E068-15216
chr152996416729964217E068-15123
chr152999045129990987E06811111
chr152999707929997166E06817739
chr152999728629997336E06817946
chr153002073630020900E06841396
chr153002093830021014E06841598
chr152992958129929724E069-49616
chr152992983629929880E069-49460
chr152992989029929972E069-49368
chr152993024729930530E069-48810
chr152997018029970913E069-8427
chr152998473729984795E0695397
chr152998485529984963E0695515
chr152998498229985134E0695642
chr152998516029985229E0695820
chr152996872429968772E070-10568
chr152996884929969575E070-9765
chr152992958129929724E071-49616
chr152992983629929880E071-49460
chr152992989029929972E071-49368
chr152995730929957353E071-21987
chr152996278629964124E071-15216
chr152996416729964217E071-15123
chr152992958129929724E072-49616
chr152992983629929880E072-49460
chr152992989029929972E072-49368
chr152993024729930530E072-48810
chr152996964929969711E072-9629
chr152996983529969879E072-9461
chr152997008329970168E072-9172
chr152997018029970913E072-8427
chr152998965629989966E07210316
chr152999014529990321E07210805
chr152999045129990987E07211111
chr152995730929957353E073-21987
chr152996278629964124E073-15216
chr152996416729964217E073-15123
chr152997008329970168E073-9172
chr152997018029970913E073-8427
chr152992958129929724E074-49616
chr152992983629929880E074-49460
chr152992989029929972E074-49368
chr152995730929957353E081-21987
chr152995751829957572E081-21768
chr152995759529958103E081-21237
chr152995875829958838E081-20502
chr152995902429959074E081-20266
chr152996278629964124E081-15216
chr152996548929965622E081-13718
chr152996569929965739E081-13601
chr152996580429965884E081-13456
chr152996597329966143E081-13197
chr152996872429968772E081-10568
chr152996884929969575E081-9765
chr152996964929969711E081-9629
chr152995730929957353E082-21987
chr152995751829957572E082-21768
chr152995759529958103E082-21237










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr152996675029967735E067-11605
chr152996777729967848E067-11492
chr152996675029967735E068-11605
chr152996777729967848E068-11492
chr152996675029967735E069-11605
chr152996777729967848E069-11492
chr152996792329968494E069-10846
chr152996667729966745E070-12595
chr152996675029967735E071-11605
chr152996777729967848E071-11492
chr152996667729966745E072-12595
chr152996675029967735E072-11605
chr152996777729967848E072-11492
chr152996792329968494E072-10846
chr152996652329966588E073-12752
chr152996667729966745E073-12595
chr152996675029967735E073-11605
chr152996777729967848E073-11492
chr152996792329968494E073-10846
chr152996675029967735E074-11605
chr152996777729967848E074-11492
chr152996667729966745E082-12595
chr152996675029967735E082-11605
chr152996777729967848E082-11492
chr152996792329968494E082-10846