rs2071293

Homo sapiens
G>A
TNXB : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0251 (7514/29900,GnomAD)
A=0194 (5671/29118,TOPMED)
A=0215 (1076/5008,1000G)
A=0292 (1125/3854,ALSPAC)
A=0307 (1139/3708,TWINSUK)
chr6:32094910 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
118 Enhancers around
32 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.32094910G>A
GRCh37.p13 chr 6NC_000006.11:g.32062687G>A
TNXB RefSeqGeneNG_008337.2:g.19465C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.3533243G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.3533349G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.3436936A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.3442521A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.3336299G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.3341884G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.3399910G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.3405530G>A

Gene: TNXB, tenascin XB(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TNXB transcript variant XBNM_019105.6:c.N/AIntron Variant
TNXB transcript variant XB-SNM_032470.3:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.980A=0.020
1000GenomesAmericanSub694G=0.640A=0.360
1000GenomesEast AsianSub1008G=0.780A=0.220
1000GenomesEuropeSub1006G=0.670A=0.330
1000GenomesGlobalStudy-wide5008G=0.785A=0.215
1000GenomesSouth AsianSub978G=0.750A=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.708A=0.292
The Genome Aggregation DatabaseAfricanSub8710G=0.944A=0.056
The Genome Aggregation DatabaseAmericanSub836G=0.590A=0.410
The Genome Aggregation DatabaseEast AsianSub1618G=0.804A=0.196
The Genome Aggregation DatabaseEuropeSub18436G=0.661A=0.338
The Genome Aggregation DatabaseGlobalStudy-wide29900G=0.748A=0.251
The Genome Aggregation DatabaseOtherSub300G=0.580A=0.420
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.805A=0.194
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.693A=0.307
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs20712935.2E-05alcoholism (heaviness of drinking)21529783

eQTL of rs2071293 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:32062687XXbac-BPG299F13.17ENSG00000272501.1G>A1.6596e-9896873Cerebellum
Chr6:32062687CYP21A1PENSG00000204338.4G>A1.1355e-1089221Cerebellum
Chr6:32062687CYP21A1PENSG00000204338.4G>A9.0047e-889221Cortex
Chr6:32062687CYP21A1PENSG00000204338.4G>A2.2428e-789221Cerebellar_Hemisphere
Chr6:32062687CYP21A1PENSG00000204338.4G>A3.5262e-889221Caudate_basal_ganglia
Chr6:32062687ATF6BENSG00000213676.6G>A8.9864e-5-33343Brain_Spinal_cord_cervical
Chr6:32062687CYP21A1PENSG00000204338.4G>A1.5384e-489221Putamen_basal_ganglia
Chr6:32062687CYP21A1PENSG00000204338.4G>A2.1327e-689221Anterior_cingulate_cortex
Chr6:32062687CYP21A1PENSG00000204338.4G>A9.3055e-689221Nucleus_accumbens_basal_ganglia

meQTL of rs2071293 in Fetal Brain

Probe ID Position Gene beta p-value
cg11032077chr6:32032728TNXB-0.0285224226308025.9798e-14

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 )
chr63205982532059869E067-2818
chr63205992732059971E067-2716
chr63206049832061316E067-1371
chr63207517832075329E06712491
chr63207533332075512E06712646
chr63208117032081311E06718483
chr63208135132081494E06718664
chr63208641532087383E06723728
chr63201412732016365E068-46322
chr63201640232016772E068-45915
chr63206049832061316E068-1371
chr63207693032077589E06814243
chr63207774832077956E06815061
chr63207897132079399E06816284
chr63207944532080700E06816758
chr63208086632081019E06818179
chr63208104032081096E06818353
chr63208117032081311E06818483
chr63208135132081494E06818664
chr63208162532082224E06818938
chr63201391032014085E069-48602
chr63201412732016365E069-46322
chr63204368732043780E069-18907
chr63204398932044519E069-18168
chr63204483432044960E069-17727
chr63206049832061316E069-1371
chr63206133832061607E069-1080
chr63207944532080700E06916758
chr63208086632081019E06918179
chr63208104032081096E06918353
chr63208117032081311E06918483
chr63208135132081494E06918664
chr63208162532082224E06918938
chr63208641532087383E06923728
chr63208745032087512E06924763
chr63208759732087647E06924910
chr63201391032014085E070-48602
chr63201412732016365E070-46322
chr63207693032077589E07014243
chr63201391032014085E071-48602
chr63201412732016365E071-46322
chr63202594932026050E071-36637
chr63204483432044960E071-17727
chr63206049832061316E071-1371
chr63206133832061607E071-1080
chr63207533332075512E07112646
chr63207774832077956E07115061
chr63207814432078317E07115457
chr63207834232078930E07115655
chr63207897132079399E07116284
chr63207944532080700E07116758
chr63208086632081019E07118179
chr63208104032081096E07118353
chr63208117032081311E07118483
chr63208135132081494E07118664
chr63208162532082224E07118938
chr63208641532087383E07123728
chr63208745032087512E07124763
chr63208759732087647E07124910
chr63201391032014085E072-48602
chr63201412732016365E072-46322
chr63205982532059869E072-2818
chr63205992732059971E072-2716
chr63206049832061316E072-1371
chr63206133832061607E072-1080
chr63207897132079399E07216284
chr63208117032081311E07218483
chr63208135132081494E07218664
chr63208641532087383E07223728
chr63201391032014085E073-48602
chr63201412732016365E073-46322
chr63201640232016772E073-45915
chr63204857932049777E073-12910
chr63205963932059689E073-2998
chr63205982532059869E073-2818
chr63205992732059971E073-2716
chr63206049832061316E073-1371
chr63207774832077956E07315061
chr63207834232078930E07315655
chr63207897132079399E07316284
chr63208086632081019E07318179
chr63208104032081096E07318353
chr63208117032081311E07318483
chr63208135132081494E07318664
chr63208641532087383E07323728
chr63208745032087512E07324763
chr63208759732087647E07324910
chr63201391032014085E074-48602
chr63201412732016365E074-46322
chr63201640232016772E074-45915
chr63202594932026050E074-36637
chr63204398932044519E074-18168
chr63204483432044960E074-17727
chr63204999432050530E074-12157
chr63205982532059869E074-2818
chr63205992732059971E074-2716
chr63206049832061316E074-1371
chr63207944532080700E07416758
chr63208086632081019E07418179
chr63208104032081096E07418353
chr63208117032081311E07418483
chr63208135132081494E07418664
chr63208162532082224E07418938
chr63208641532087383E07423728
chr63208745032087512E07424763
chr63208759732087647E07424910
chr63201391032014085E081-48602
chr63206049832061316E081-1371
chr63206133832061607E081-1080
chr63206166532061725E081-962
chr63206180232061854E081-833
chr63206237632062423E081-264
chr63206320832063359E081521
chr63206514332065344E0812456
chr63210478932104834E08142102
chr63201391032014085E082-48602
chr63202594932026050E082-36637
chr63205401132054089E082-8598










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63206408632064136E0671399
chr63206420132064492E0671514
chr63206453732064587E0671850
chr63209535532096667E06732668
chr63209686232098780E06734175
chr63206408632064136E0681399
chr63206420132064492E0681514
chr63206453732064587E0681850
chr63209535532096667E06832668
chr63209686232098780E06834175
chr63206408632064136E0691399
chr63209535532096667E06932668
chr63209686232098780E06934175
chr63206408632064136E0701399
chr63209535532096667E07032668
chr63209686232098780E07034175
chr63209535532096667E07132668
chr63209686232098780E07134175
chr63206408632064136E0721399
chr63209535532096667E07232668
chr63209686232098780E07234175
chr63206408632064136E0731399
chr63206420132064492E0731514
chr63206453732064587E0731850
chr63209535532096667E07332668
chr63209686232098780E07334175
chr63209535532096667E07432668
chr63209686232098780E07434175
chr63209686232098780E08134175
chr63206420132064492E0821514
chr63209535532096667E08232668
chr63209686232098780E08234175