rs3132580

Homo sapiens
G>A
DPCR1 : Missense Variant
HCG21 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0080 (9717/120978,ExAC)
A=0101 (3027/29962,GnomAD)
A=0095 (2782/29118,TOPMED)
G==0110 (1443/13006,GO-ESP)
A=0038 (192/5008,1000G)
A=0162 (623/3854,ALSPAC)
A=0169 (625/3708,TWINSUK)
chr6:30952347 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
44 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.30952347G>A
GRCh37.p13 chr 6NC_000006.11:g.30920124G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.2431922A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.2432028A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.2207500G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.2213096G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.2208654G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.2214239G>A

Gene: DPCR1, diffuse panbronchiolitis critical region 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MUCL3 transcriptNM_080870.3:c.388...NM_080870.3:c.3883G>AE [GAG]> K [AAG]Coding Sequence Variant
diffuse panbronchiolitis critical region protein 1 precursorNP_543146.2:p.Glu...NP_543146.2:p.Glu1295LysE [Glu]> K [Lys]Missense Variant

Gene: HCG21, uncharacterized HCG21(minus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
HCG21 transcript variant X1XR_926690.2:n.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.962A=0.038
1000GenomesAmericanSub694G=0.970A=0.030
1000GenomesEast AsianSub1008G=0.984A=0.016
1000GenomesEuropeSub1006G=0.904A=0.096
1000GenomesGlobalStudy-wide5008G=0.962A=0.038
1000GenomesSouth AsianSub978G=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.838A=0.162
The Exome Aggregation ConsortiumAmericanSub21840G=0.954A=0.045
The Exome Aggregation ConsortiumAsianSub25116G=0.982A=0.017
The Exome Aggregation ConsortiumEuropeSub73116G=0.887A=0.112
The Exome Aggregation ConsortiumGlobalStudy-wide120978G=0.919A=0.080
The Exome Aggregation ConsortiumOtherSub906G=0.940A=0.060
The Genome Aggregation DatabaseAfricanSub8724G=0.937A=0.063
The Genome Aggregation DatabaseAmericanSub838G=0.960A=0.040
The Genome Aggregation DatabaseEast AsianSub1618G=0.979A=0.021
The Genome Aggregation DatabaseEuropeSub18480G=0.870A=0.129
The Genome Aggregation DatabaseGlobalStudy-wide29962G=0.899A=0.101
The Genome Aggregation DatabaseOtherSub302G=0.930A=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.904A=0.095
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.831A=0.169
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
rs31325800.00061alcohol dependence20201924

eQTL of rs3132580 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:30920124VARS2ENSG00000137411.12G>A1.6866e-1038142Cerebellum
Chr6:30920124CCHCR1ENSG00000204536.9G>A1.0258e-9-205891Cerebellum
Chr6:30920124VARS2ENSG00000137411.12G>A3.3720e-1138142Frontal_Cortex_BA9
Chr6:30920124VARS2ENSG00000137411.12G>A6.0075e-1438142Cortex
Chr6:30920124VARS2ENSG00000137411.12G>A1.6124e-838142Cerebellar_Hemisphere
Chr6:30920124CCHCR1ENSG00000204536.9G>A6.3052e-8-205891Cerebellar_Hemisphere
Chr6:30920124MICBENSG00000204516.5G>A1.7000e-27-542534Cerebellar_Hemisphere
Chr6:30920124VARS2ENSG00000137411.12G>A6.3004e-1138142Hippocampus
Chr6:30920124VARS2ENSG00000137411.12G>A7.9865e-1338142Anterior_cingulate_cortex
Chr6:30920124VARS2ENSG00000137411.12G>A1.5180e-938142Amygdala

meQTL of rs3132580 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 )
chr63087731330877404E067-42720
chr63088383630883886E067-36238
chr63088398330884086E067-36038
chr63088492330884995E067-35129
chr63088506130885101E067-35023
chr63088087330880923E068-39201
chr63088097130881214E068-38910
chr63088383630883886E068-36238
chr63088398330884086E069-36038
chr63088492330884995E069-35129
chr63088506130885101E069-35023
chr63088097130881214E070-38910
chr63088383630883886E070-36238
chr63088398330884086E070-36038
chr63087731330877404E071-42720
chr63088097130881214E071-38910
chr63088383630883886E071-36238
chr63088398330884086E071-36038
chr63088492330884995E071-35129
chr63092239430922784E0712270
chr63087731330877404E072-42720
chr63088383630883886E072-36238
chr63088398330884086E072-36038
chr63088492330884995E072-35129
chr63088506130885101E072-35023
chr63087731330877404E073-42720
chr63088383630883886E073-36238
chr63088398330884086E073-36038
chr63092916230929212E0739038
chr63092925430929392E0739130
chr63087731330877404E074-42720
chr63088097130881214E074-38910
chr63088383630883886E074-36238
chr63088398330884086E074-36038
chr63088492330884995E074-35129
chr63088506130885101E074-35023
chr63088649830886764E074-33360
chr63088097130881214E081-38910
chr63088383630883886E081-36238
chr63088398330884086E081-36038
chr63087731330877404E082-42720
chr63087794930877994E082-42130
chr63088383630883886E082-36238
chr63088398330884086E082-36038










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63087549130876574E067-43550
chr63092305630924027E0672932
chr63087549130876574E068-43550
chr63092305630924027E0682932
chr63087533030875389E069-44735
chr63087549130876574E069-43550
chr63087549130876574E070-43550
chr63087549130876574E071-43550
chr63092305630924027E0712932
chr63087515030875327E072-44797
chr63087533030875389E072-44735
chr63087549130876574E072-43550
chr63092305630924027E0722932
chr63087549130876574E073-43550
chr63092305630924027E0732932
chr63087549130876574E074-43550
chr63091997030920024E074-100
chr63092305630924027E0742932
chr63087549130876574E081-43550
chr63087549130876574E082-43550
chr63092305630924027E0822932