rs1997247

Homo sapiens
G>A
TMEM17 : Intron Variant
LOC105374764 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0111 (3335/29964,GnomAD)
A=0076 (2239/29116,TOPMED)
A=0112 (563/5008,1000G)
A=0127 (491/3854,ALSPAC)
A=0125 (464/3708,TWINSUK)
chr2:62530420 (GRCh38.p7) (2p15)
ND
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.62530420G>A
GRCh37.p13 chr 2NC_000002.11:g.62757555G>A

Gene: TMEM17, transmembrane protein 17(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TMEM17 transcriptNM_198276.2:c.N/AGenic Upstream Transcript Variant
TMEM17 transcript variant X1XM_017003575.1:c.N/AIntron Variant
TMEM17 transcript variant X3XM_011532693.2:c.N/AGenic Upstream Transcript Variant
TMEM17 transcript variant X4XM_011532694.2:c.N/AGenic Upstream Transcript Variant

Gene: LOC105374764, uncharacterized LOC105374764(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374764 transcript variant X1XR_001739094.1:n.N/AIntron Variant
LOC105374764 transcript variant X3XR_001739095.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.977A=0.023
1000GenomesAmericanSub694G=0.910A=0.090
1000GenomesEast AsianSub1008G=0.791A=0.209
1000GenomesEuropeSub1006G=0.880A=0.120
1000GenomesGlobalStudy-wide5008G=0.888A=0.112
1000GenomesSouth AsianSub978G=0.860A=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.873A=0.127
The Genome Aggregation DatabaseAfricanSub8726G=0.960A=0.040
The Genome Aggregation DatabaseAmericanSub838G=0.900A=0.100
The Genome Aggregation DatabaseEast AsianSub1610G=0.779A=0.221
The Genome Aggregation DatabaseEuropeSub18488G=0.863A=0.136
The Genome Aggregation DatabaseGlobalStudy-wide29964G=0.888A=0.111
The Genome Aggregation DatabaseOtherSub302G=0.940A=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.923A=0.076
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.875A=0.125
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
rs19972479.7E-07alcohol and nictotine co-dependence20158304

eQTL of rs1997247 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 rs1997247 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 )
chr26271613462716649E067-40906
chr26271286962713852E068-43703
chr26280501562806761E06847460
chr26271613462716649E069-40906
chr26271286962713852E070-43703
chr26275686162756911E070-644
chr26271286962713852E071-43703
chr26271613462716649E071-40906
chr26273199762732049E071-25506
chr26273206862732179E071-25376
chr26275507362755424E071-2131
chr26271598162716103E072-41452
chr26271613462716649E072-40906
chr26271613462716649E074-40906







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr26273221362733986E067-23569
chr26279798862798117E06740433
chr26279812762798669E06740572
chr26273221362733986E068-23569
chr26279798862798117E06840433
chr26279812762798669E06840572
chr26273221362733986E069-23569
chr26273221362733986E070-23569
chr26279798862798117E07040433
chr26279812762798669E07040572
chr26273221362733986E071-23569
chr26273221362733986E072-23569
chr26279798862798117E07240433
chr26279812762798669E07240572
chr26273221362733986E073-23569
chr26273221362733986E074-23569
chr26273221362733986E082-23569
chr26279798862798117E08240433
chr26279812762798669E08240572