rs2479955

Homo sapiens
A>G
TEX29 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0204 (6131/29952,GnomAD)
A==0182 (5326/29118,TOPMED)
G=0195 (1117/5734,GO-ESP)
A==0189 (949/5008,1000G)
A==0192 (740/3854,ALSPAC)
A==0198 (734/3708,TWINSUK)
chr13:111328131 (GRCh38.p7) (13q34)
AD
GWASdb2
1   publication(s)
See rs on genome
61 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.111328131A>G
GRCh37.p13 chr 13NC_000013.10:g.111980478A>G

Gene: TEX29, testis expressed 29(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TEX29 transcript variant 1NM_001303133.1:c.N/AIntron Variant
TEX29 transcript variant 2NM_152324.2:c.N/AIntron Variant
TEX29 transcript variant X1XM_017020387.1:c.N/AIntron Variant
TEX29 transcript variant X2XM_017020388.1:c.N/AIntron Variant
TEX29 transcript variant X3XR_001749478.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.232G=0.768
1000GenomesAmericanSub694A=0.100G=0.900
1000GenomesEast AsianSub1008A=0.142G=0.858
1000GenomesEuropeSub1006A=0.191G=0.809
1000GenomesGlobalStudy-wide5008A=0.189G=0.811
1000GenomesSouth AsianSub978A=0.240G=0.760
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.192G=0.808
The Genome Aggregation DatabaseAfricanSub8708A=0.207G=0.793
The Genome Aggregation DatabaseAmericanSub836A=0.090G=0.910
The Genome Aggregation DatabaseEast AsianSub1618A=0.118G=0.882
The Genome Aggregation DatabaseEuropeSub18488A=0.217G=0.782
The Genome Aggregation DatabaseGlobalStudy-wide29952A=0.204G=0.795
The Genome Aggregation DatabaseOtherSub302A=0.150G=0.850
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.182G=0.817
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.198G=0.802
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
rs24799550.00047alcohol dependence20201924

eQTL of rs2479955 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 rs2479955 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 )
chr13111931724111931783E067-48695
chr13111932959111935073E067-45405
chr13111936041111936112E067-44366
chr13111936460111936664E067-43814
chr13111939024111939095E067-41383
chr13111932959111935073E068-45405
chr13111950867111950917E068-29561
chr13111931003111931161E069-49317
chr13111931168111931673E069-48805
chr13111931724111931783E069-48695
chr13111932739111932953E069-47525
chr13111932959111935073E069-45405
chr13111936460111936664E069-43814
chr13111979363111979413E070-1065
chr13111980819111980882E070341
chr13111981020111981090E070542
chr13111987397111987447E0706919
chr13111987473111987557E0706995
chr13111987628111988023E0707150
chr13111988119111988169E0707641
chr13111988214111988264E0707736
chr13112022696112022736E07042218
chr13112022791112022841E07042313
chr13112023217112023279E07042739
chr13112023317112023387E07042839
chr13112023598112023839E07043120
chr13112024048112024130E07043570
chr13111935403111935606E071-44872
chr13111936041111936112E071-44366
chr13111936460111936664E071-43814
chr13111936809111936873E071-43605
chr13111936910111936960E071-43518
chr13111937021111937114E071-43364
chr13111931724111931783E072-48695
chr13111931815111932468E072-48010
chr13111932545111932620E072-47858
chr13111932739111932953E072-47525
chr13111932959111935073E072-45405
chr13111936460111936664E072-43814
chr13111936809111936873E072-43605
chr13111936910111936960E072-43518
chr13111937021111937114E072-43364
chr13111945563111945750E072-34728
chr13111936041111936112E073-44366
chr13111938624111938790E073-41688
chr13111939024111939095E073-41383
chr13111939206111939256E073-41222
chr13111987628111988023E0747150
chr13111980819111980882E081341
chr13111987151111987208E0816673
chr13111987397111987447E0816919
chr13111987473111987557E0816995
chr13111987628111988023E0817150
chr13111988119111988169E0817641
chr13111988214111988264E0817736
chr13111996676111997619E08116198
chr13112012232112012384E08131754
chr13112012521112012658E08132043
chr13111987628111988023E0827150
chr13111988119111988169E0827641
chr13111988214111988264E0827736