rs3131921

Homo sapiens
T>C
DPCR1 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0122 (3652/29894,GnomAD)
C=0106 (3094/29118,TOPMED)
C=0087 (437/5008,1000G)
C=0165 (636/3854,ALSPAC)
C=0170 (632/3708,TWINSUK)
chr6:30939558 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
59 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.30939558T>C
GRCh37.p13 chr 6NC_000006.11:g.30907335T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.2419142C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.2419248C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.2194712T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.2200308T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.2195866T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.2201451T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.2283691T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.2289276T>C

Gene: DPCR1, diffuse panbronchiolitis critical region 1(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
MUCL3 transcriptNM_080870.3:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.946C=0.054
1000GenomesAmericanSub694T=0.950C=0.050
1000GenomesEast AsianSub1008T=0.802C=0.198
1000GenomesEuropeSub1006T=0.895C=0.105
1000GenomesGlobalStudy-wide5008T=0.913C=0.087
1000GenomesSouth AsianSub978T=0.980C=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.835C=0.165
The Genome Aggregation DatabaseAfricanSub8706T=0.925C=0.075
The Genome Aggregation DatabaseAmericanSub838T=0.910C=0.090
The Genome Aggregation DatabaseEast AsianSub1612T=0.769C=0.231
The Genome Aggregation DatabaseEuropeSub18436T=0.862C=0.137
The Genome Aggregation DatabaseGlobalStudy-wide29894T=0.877C=0.122
The Genome Aggregation DatabaseOtherSub302T=0.930C=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.893C=0.106
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.830C=0.170
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
rs31319210.00048alcohol dependence20201924

eQTL of rs3131921 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:30907335VARS2ENSG00000137411.12T>C1.6866e-1025353Cerebellum
Chr6:30907335CCHCR1ENSG00000204536.9T>C1.0258e-9-218680Cerebellum
Chr6:30907335VARS2ENSG00000137411.12T>C3.3720e-1125353Frontal_Cortex_BA9
Chr6:30907335VARS2ENSG00000137411.12T>C5.2616e-1125353Hypothalamus
Chr6:30907335VARS2ENSG00000137411.12T>C6.0075e-1425353Cortex
Chr6:30907335VARS2ENSG00000137411.12T>C1.6124e-825353Cerebellar_Hemisphere
Chr6:30907335CCHCR1ENSG00000204536.9T>C6.3052e-8-218680Cerebellar_Hemisphere
Chr6:30907335MICBENSG00000204516.5T>C1.7000e-27-555323Cerebellar_Hemisphere
Chr6:30907335VARS2ENSG00000137411.12T>C6.3004e-1125353Hippocampus
Chr6:30907335VARS2ENSG00000137411.12T>C7.9865e-1325353Anterior_cingulate_cortex
Chr6:30907335HLA-JENSG00000204622.6T>C4.2891e-9932161Nucleus_accumbens_basal_ganglia
Chr6:30907335VARS2ENSG00000137411.12T>C1.5180e-925353Amygdala

meQTL of rs3131921 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 )
chr63085755430857647E067-49688
chr63085767230858400E067-48935
chr63087731330877404E067-29931
chr63088383630883886E067-23449
chr63088398330884086E067-23249
chr63088492330884995E067-22340
chr63088506130885101E067-22234
chr63085755430857647E068-49688
chr63088087330880923E068-26412
chr63088097130881214E068-26121
chr63088383630883886E068-23449
chr63088398330884086E069-23249
chr63088492330884995E069-22340
chr63088506130885101E069-22234
chr63085755430857647E070-49688
chr63085767230858400E070-48935
chr63088097130881214E070-26121
chr63088383630883886E070-23449
chr63088398330884086E070-23249
chr63086228230862332E071-45003
chr63086306330863186E071-44149
chr63087731330877404E071-29931
chr63088097130881214E071-26121
chr63088383630883886E071-23449
chr63088398330884086E071-23249
chr63088492330884995E071-22340
chr63092239430922784E07115059
chr63086080430860922E072-46413
chr63087731330877404E072-29931
chr63088383630883886E072-23449
chr63088398330884086E072-23249
chr63088492330884995E072-22340
chr63088506130885101E072-22234
chr63085755430857647E073-49688
chr63085767230858400E073-48935
chr63087731330877404E073-29931
chr63088383630883886E073-23449
chr63088398330884086E073-23249
chr63092916230929212E07321827
chr63092925430929392E07321919
chr63086080430860922E074-46413
chr63086228230862332E074-45003
chr63087731330877404E074-29931
chr63088097130881214E074-26121
chr63088383630883886E074-23449
chr63088398330884086E074-23249
chr63088492330884995E074-22340
chr63088506130885101E074-22234
chr63088649830886764E074-20571
chr63085755430857647E081-49688
chr63085767230858400E081-48935
chr63088097130881214E081-26121
chr63088383630883886E081-23449
chr63088398330884086E081-23249
chr63085767230858400E082-48935
chr63087731330877404E082-29931
chr63087794930877994E082-29341
chr63088383630883886E082-23449
chr63088398330884086E082-23249










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63087549130876574E067-30761
chr63092305630924027E06715721
chr63087549130876574E068-30761
chr63092305630924027E06815721
chr63087533030875389E069-31946
chr63087549130876574E069-30761
chr63087549130876574E070-30761
chr63087549130876574E071-30761
chr63092305630924027E07115721
chr63087515030875327E072-32008
chr63087533030875389E072-31946
chr63087549130876574E072-30761
chr63092305630924027E07215721
chr63087549130876574E073-30761
chr63092305630924027E07315721
chr63087549130876574E074-30761
chr63091997030920024E07412635
chr63092305630924027E07415721
chr63087549130876574E081-30761
chr63087549130876574E082-30761
chr63092305630924027E08215721