rs845104

Homo sapiens
A>T
LOC105378531 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0486 (14548/29910,GnomAD)
T=0465 (13543/29118,TOPMED)
A==0445 (2229/5008,1000G)
A==0490 (1890/3854,ALSPAC)
T=0499 (1852/3708,TWINSUK)
chr10:123423467 (GRCh38.p7) (10q26.13)
ND
GWASdb2
1   publication(s)
See rs on genome
44 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.123423467A>T
GRCh37.p13 chr 10NC_000010.10:g.125182983A>T

Gene: LOC105378531, uncharacterized LOC105378531(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378531 transcript variant X5XR_001747617.1:n....XR_001747617.1:n.2450A>TA>TNon Coding Transcript Variant
LOC105378531 transcript variant X8XR_001747619.1:n....XR_001747619.1:n.2450A>TA>TNon Coding Transcript Variant
LOC105378531 transcript variant X2XR_001747614.1:n.N/AIntron Variant
LOC105378531 transcript variant X4XR_001747615.1:n.N/AIntron Variant
LOC105378531 transcript variant X6XR_001747616.1:n.N/AGenic Upstream Transcript Variant
LOC105378531 transcript variant X10XR_001747618.1:n.N/AGenic Upstream Transcript Variant
LOC105378531 transcript variant X11XR_001747620.1:n.N/AGenic Upstream Transcript Variant
LOC105378531 transcript variant X8XR_946391.2:n.N/AGenic Upstream Transcript Variant
LOC105378531 transcript variant X5XR_946398.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.640T=0.360
1000GenomesAmericanSub694A=0.370T=0.630
1000GenomesEast AsianSub1008A=0.207T=0.793
1000GenomesEuropeSub1006A=0.523T=0.477
1000GenomesGlobalStudy-wide5008A=0.445T=0.555
1000GenomesSouth AsianSub978A=0.400T=0.600
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.490T=0.510
The Genome Aggregation DatabaseAfricanSub8716A=0.646T=0.354
The Genome Aggregation DatabaseAmericanSub836A=0.330T=0.670
The Genome Aggregation DatabaseEast AsianSub1612A=0.212T=0.788
The Genome Aggregation DatabaseEuropeSub18444A=0.485T=0.514
The Genome Aggregation DatabaseGlobalStudy-wide29910A=0.513T=0.486
The Genome Aggregation DatabaseOtherSub302A=0.500T=0.500
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.534T=0.465
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.501T=0.499
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs8451040.000722nicotine dependence17158188

eQTL of rs845104 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 rs845104 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 )
chr10125140298125140504E067-42479
chr10125140551125140631E067-42352
chr10125188134125188273E0675151
chr10125188601125188743E0685618
chr10125188886125189049E0685903
chr10125168802125168984E070-13999
chr10125169061125169275E070-13708
chr10125169367125169446E070-13537
chr10125188134125188273E0705151
chr10125189109125190046E0706126
chr10125229915125230538E07046932
chr10125231465125231749E07048482
chr10125189109125190046E0716126
chr10125140298125140504E072-42479
chr10125229769125229885E07246786
chr10125229915125230538E07246932
chr10125157893125157983E074-25000
chr10125158829125158924E074-24059
chr10125229769125229885E07446786
chr10125229915125230538E07446932
chr10125133224125133425E081-49558
chr10125133528125133587E081-49396
chr10125133635125133689E081-49294
chr10125168642125168748E081-14235
chr10125168802125168984E081-13999
chr10125169061125169275E081-13708
chr10125169367125169446E081-13537
chr10125186339125186573E0813356
chr10125186642125186741E0813659
chr10125187014125187188E0814031
chr10125188134125188273E0815151
chr10125188601125188743E0815618
chr10125188886125189049E0815903
chr10125229769125229885E08146786
chr10125229915125230538E08146932
chr10125231465125231749E08148482
chr10125232018125232164E08149035
chr10125232171125232600E08149188
chr10125168642125168748E082-14235
chr10125168802125168984E082-13999
chr10125169061125169275E082-13708
chr10125169367125169446E082-13537
chr10125185503125185553E0822520
chr10125188134125188273E0825151