rs2479956

Homo sapiens
T>C
TEX29 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0225 (6753/29934,GnomAD)
T==0215 (6287/29118,TOPMED)
T==0210 (1052/5008,1000G)
T==0195 (750/3854,ALSPAC)
T==0200 (742/3708,TWINSUK)
chr13:111329052 (GRCh38.p7) (13q34)
AD
GWASdb2
1   publication(s)
See rs on genome
59 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.111329052T>C
GRCh37.p13 chr 13NC_000013.10:g.111981399T>C

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
1000GenomesAfricanSub1322T=0.297C=0.703
1000GenomesAmericanSub694T=0.130C=0.870
1000GenomesEast AsianSub1008T=0.141C=0.859
1000GenomesEuropeSub1006T=0.189C=0.811
1000GenomesGlobalStudy-wide5008T=0.210C=0.790
1000GenomesSouth AsianSub978T=0.240C=0.760
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.195C=0.805
The Genome Aggregation DatabaseAfricanSub8704T=0.272C=0.728
The Genome Aggregation DatabaseAmericanSub836T=0.110C=0.890
The Genome Aggregation DatabaseEast AsianSub1622T=0.116C=0.884
The Genome Aggregation DatabaseEuropeSub18470T=0.219C=0.780
The Genome Aggregation DatabaseGlobalStudy-wide29934T=0.225C=0.774
The Genome Aggregation DatabaseOtherSub302T=0.160C=0.840
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.215C=0.784
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.200C=0.800
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
rs24799560.00056alcohol dependence20201924

eQTL of rs2479956 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 rs2479956 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 )
chr13111931724111931783E067-49616
chr13111932959111935073E067-46326
chr13111936041111936112E067-45287
chr13111936460111936664E067-44735
chr13111939024111939095E067-42304
chr13111932959111935073E068-46326
chr13111950867111950917E068-30482
chr13111931724111931783E069-49616
chr13111932739111932953E069-48446
chr13111932959111935073E069-46326
chr13111936460111936664E069-44735
chr13111979363111979413E070-1986
chr13111980819111980882E070-517
chr13111981020111981090E070-309
chr13111987397111987447E0705998
chr13111987473111987557E0706074
chr13111987628111988023E0706229
chr13111988119111988169E0706720
chr13111988214111988264E0706815
chr13112022696112022736E07041297
chr13112022791112022841E07041392
chr13112023217112023279E07041818
chr13112023317112023387E07041918
chr13112023598112023839E07042199
chr13112024048112024130E07042649
chr13111935403111935606E071-45793
chr13111936041111936112E071-45287
chr13111936460111936664E071-44735
chr13111936809111936873E071-44526
chr13111936910111936960E071-44439
chr13111937021111937114E071-44285
chr13111931724111931783E072-49616
chr13111931815111932468E072-48931
chr13111932545111932620E072-48779
chr13111932739111932953E072-48446
chr13111932959111935073E072-46326
chr13111936460111936664E072-44735
chr13111936809111936873E072-44526
chr13111936910111936960E072-44439
chr13111937021111937114E072-44285
chr13111945563111945750E072-35649
chr13111936041111936112E073-45287
chr13111938624111938790E073-42609
chr13111939024111939095E073-42304
chr13111939206111939256E073-42143
chr13111987628111988023E0746229
chr13111980819111980882E081-517
chr13111987151111987208E0815752
chr13111987397111987447E0815998
chr13111987473111987557E0816074
chr13111987628111988023E0816229
chr13111988119111988169E0816720
chr13111988214111988264E0816815
chr13111996676111997619E08115277
chr13112012232112012384E08130833
chr13112012521112012658E08131122
chr13111987628111988023E0826229
chr13111988119111988169E0826720
chr13111988214111988264E0826815