rs10040610

Homo sapiens
T>C
LOC105374638 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0154 (4640/29948,GnomAD)
C=0156 (4570/29118,TOPMED)
C=0211 (1059/5008,1000G)
C=0101 (390/3854,ALSPAC)
C=0111 (411/3708,TWINSUK)
chr5:6353702 (GRCh38.p7) (5p15.31)
AD
GWASdb2
2   publication(s)
See rs on genome
19 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.6353702T>C
GRCh37.p13 chr 5NC_000005.9:g.6353815T>C

Gene: LOC105374638, uncharacterized LOC105374638(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374638 transcript variant X1XR_001742588.1:n....XR_001742588.1:n.4800A>GA>GNon Coding Transcript Variant
LOC105374638 transcript variant X2XR_001742589.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.757C=0.243
1000GenomesAmericanSub694T=0.840C=0.160
1000GenomesEast AsianSub1008T=0.675C=0.325
1000GenomesEuropeSub1006T=0.892C=0.108
1000GenomesGlobalStudy-wide5008T=0.789C=0.211
1000GenomesSouth AsianSub978T=0.810C=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.899C=0.101
The Genome Aggregation DatabaseAfricanSub8722T=0.786C=0.214
The Genome Aggregation DatabaseAmericanSub836T=0.860C=0.140
The Genome Aggregation DatabaseEast AsianSub1620T=0.703C=0.297
The Genome Aggregation DatabaseEuropeSub18468T=0.883C=0.116
The Genome Aggregation DatabaseGlobalStudy-wide29948T=0.845C=0.154
The Genome Aggregation DatabaseOtherSub302T=0.910C=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.843C=0.156
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.889C=0.111
PMID Title Author Journal
22384118Integrative genomic analysis reveals extended germline homozygosity with lung cancer risk in the PLCO cohort.Orloff MSPLoS One
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs100406100.000154alcohol consumption (maxi-drinks)24277619

eQTL of rs10040610 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 rs10040610 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 )
chr563335896333855E067-19960
chr563335896333855E068-19960
chr563335896333855E069-19960
chr563196606319710E070-34105
chr563200606320189E070-33626
chr563383946338504E070-15311
chr563389406339014E070-14801
chr563392506339300E070-14515
chr563335896333855E071-19960
chr563335896333855E073-19960
chr563605736360702E0736758
chr563335896333855E074-19960
chr563174576317749E081-36066
chr563178696318069E081-35746
chr563071266307230E082-46585
chr563174576317749E082-36066
chr563178696318069E082-35746
chr563194366319565E082-34250
chr563196606319710E082-34105









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr563776656377813E06723850
chr563778846379147E06724069
chr563776656377813E06823850
chr563778846379147E06824069
chr563776656377813E06923850
chr563778846379147E06924069
chr563776656377813E07023850
chr563778846379147E07024069
chr563776656377813E07123850
chr563778846379147E07124069
chr563776656377813E07223850
chr563778846379147E07224069
chr563776656377813E07323850
chr563778846379147E07324069
chr563776656377813E07423850
chr563778846379147E07424069
chr563776656377813E08123850
chr563778846379147E08124069
chr563776656377813E08223850
chr563778846379147E08224069