rs9860628

Homo sapiens
C>T
LOC105377157 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0302 (9040/29906,GnomAD)
C==0378 (11014/29118,TOPMED)
C==0320 (1605/5008,1000G)
C==0145 (557/3854,ALSPAC)
C==0134 (498/3708,TWINSUK)
chr3:71993849 (GRCh38.p7) (3p13)
AD
GWASdb2
1   publication(s)
See rs on genome
99 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.71993849C>T
GRCh37.p13 chr 3NC_000003.11:g.72043000C>T

Gene: LOC105377157, uncharacterized LOC105377157(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377157 transcriptXR_940957.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.717T=0.283
1000GenomesAmericanSub694C=0.230T=0.770
1000GenomesEast AsianSub1008C=0.235T=0.765
1000GenomesEuropeSub1006C=0.142T=0.858
1000GenomesGlobalStudy-wide5008C=0.320T=0.680
1000GenomesSouth AsianSub978C=0.120T=0.880
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.145T=0.855
The Genome Aggregation DatabaseAfricanSub8668C=0.653T=0.347
The Genome Aggregation DatabaseAmericanSub838C=0.220T=0.780
The Genome Aggregation DatabaseEast AsianSub1610C=0.231T=0.769
The Genome Aggregation DatabaseEuropeSub18488C=0.150T=0.849
The Genome Aggregation DatabaseGlobalStudy-wide29906C=0.302T=0.697
The Genome Aggregation DatabaseOtherSub302C=0.150T=0.850
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.378T=0.621
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.134T=0.866
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
rs98606280.00079alcohol dependence20201924

eQTL of rs9860628 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 rs9860628 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 )
chr37200453172005318E067-37682
chr37200532672005425E067-37575
chr37208983472089992E06746834
chr37209018272090365E06747182
chr37209040472090491E06747404
chr37209055272091059E06747552
chr37200437972004430E068-38570
chr37200453172005318E068-37682
chr37200532672005425E068-37575
chr37200599172006130E068-36870
chr37202261772022753E068-20247
chr37202283672023257E068-19743
chr37208983472089992E06846834
chr37209018272090365E06847182
chr37209040472090491E06847404
chr37209055272091059E06847552
chr37209159672091861E06848596
chr37200437972004430E069-38570
chr37200453172005318E069-37682
chr37200532672005425E069-37575
chr37200599172006130E069-36870
chr37202237972022429E069-20571
chr37202261772022753E069-20247
chr37202283672023257E069-19743
chr37202556172025684E069-17316
chr37208983472089992E06946834
chr37209018272090365E06947182
chr37209040472090491E06947404
chr37209055272091059E06947552
chr37209159672091861E06948596
chr37200437972004430E070-38570
chr37200453172005318E070-37682
chr37200532672005425E070-37575
chr37208983472089992E07046834
chr37209018272090365E07047182
chr37209040472090491E07047404
chr37209055272091059E07047552
chr37209159672091861E07048596
chr37200437972004430E071-38570
chr37200453172005318E071-37682
chr37200532672005425E071-37575
chr37202217072022220E071-20780
chr37202237972022429E071-20571
chr37202261772022753E071-20247
chr37202556172025684E071-17316
chr37208983472089992E07146834
chr37209018272090365E07147182
chr37209040472090491E07147404
chr37209055272091059E07147552
chr37209159672091861E07148596
chr37200437972004430E072-38570
chr37200532672005425E072-37575
chr37200599172006130E072-36870
chr37202261772022753E072-20247
chr37208052972080690E07237529
chr37208983472089992E07246834
chr37209040472090491E07247404
chr37209055272091059E07247552
chr37209159672091861E07248596
chr37200437972004430E073-38570
chr37200453172005318E073-37682
chr37200532672005425E073-37575
chr37202261772022753E073-20247
chr37209018272090365E07347182
chr37209040472090491E07347404
chr37209055272091059E07347552
chr37200437972004430E074-38570
chr37200453172005318E074-37682
chr37200532672005425E074-37575
chr37200599172006130E074-36870
chr37202217072022220E074-20780
chr37202237972022429E074-20571
chr37202261772022753E074-20247
chr37202283672023257E074-19743
chr37209018272090365E07447182
chr37209040472090491E07447404
chr37209055272091059E07447552
chr37209159672091861E07448596
chr37200372972003840E081-39160
chr37200437972004430E081-38570
chr37200453172005318E081-37682
chr37200532672005425E081-37575
chr37201759172017682E081-25318
chr37201781872017989E081-25011
chr37205927672059479E08116276
chr37205962372059769E08116623
chr37206158072061751E08118580
chr37208934172089462E08146341
chr37208983472089992E08146834
chr37209018272090365E08147182
chr37209040472090491E08147404
chr37209055272091059E08147552
chr37200437972004430E082-38570
chr37200453172005318E082-37682
chr37208934172089462E08246341
chr37208983472089992E08246834
chr37209018272090365E08247182
chr37209040472090491E08247404
chr37209055272091059E08247552