rs17042708

Homo sapiens
A>G
LOC105376921 : Intron Variant
LOC107986040 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0140 (4190/29902,GnomAD)
G=0126 (3685/29118,TOPMED)
G=0215 (1079/5008,1000G)
G=0129 (497/3854,ALSPAC)
G=0113 (420/3708,TWINSUK)
chr3:66543 (GRCh38.p7) (3p26.3)
AD
GWASdb2
1   publication(s)
See rs on genome
101 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.66543A>G
GRCh37.p13 chr 3NC_000003.11:g.108226A>G

Gene: LOC105376921, uncharacterized LOC105376921(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105376921 transcriptXR_940533.1:n.N/AIntron Variant

Gene: LOC107986040, uncharacterized LOC107986040(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC107986040 transcriptXR_001740550.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.899G=0.101
1000GenomesAmericanSub694A=0.800G=0.200
1000GenomesEast AsianSub1008A=0.565G=0.435
1000GenomesEuropeSub1006A=0.872G=0.128
1000GenomesGlobalStudy-wide5008A=0.785G=0.215
1000GenomesSouth AsianSub978A=0.750G=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.871G=0.129
The Genome Aggregation DatabaseAfricanSub8700A=0.893G=0.107
The Genome Aggregation DatabaseAmericanSub836A=0.770G=0.230
The Genome Aggregation DatabaseEast AsianSub1584A=0.547G=0.453
The Genome Aggregation DatabaseEuropeSub18480A=0.874G=0.125
The Genome Aggregation DatabaseGlobalStudy-wide29902A=0.859G=0.140
The Genome Aggregation DatabaseOtherSub302A=0.870G=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.873G=0.126
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.887G=0.113
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
rs170427080.00062alcohol dependence20201924

eQTL of rs17042708 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 rs17042708 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 )
chr3104810105451E067-2775
chr3114174114280E0675948
chr3114437114799E0676211
chr3141018141128E06732792
chr3114174114280E0685948
chr3114437114799E0686211
chr3114802115003E0686576
chr3115137115254E0686911
chr3115361115440E0687135
chr3139390139586E06831164
chr3139704139834E06831478
chr3141018141128E06832792
chr3141277141526E06833051
chr3104810105451E069-2775
chr3105525105633E069-2593
chr3114174114280E0695948
chr3114437114799E0696211
chr3114802115003E0696576
chr3115137115254E0696911
chr3115361115440E0697135
chr3141018141128E06932792
chr3114174114280E0705948
chr3114437114799E0706211
chr3114802115003E0706576
chr3115137115254E0706911
chr3115361115440E0707135
chr3116283116363E0708057
chr3116414116901E0708188
chr3117032117204E0708806
chr3117319117416E0709093
chr3117466117544E0709240
chr3123630123786E07015404
chr3123847123912E07015621
chr3124839125153E07016613
chr3139183139333E07030957
chr3139390139586E07031164
chr3139704139834E07031478
chr3142138142206E07033912
chr3144310144411E07036084
chr3145812145986E07037586
chr3152159152209E07043933
chr3152592152664E07044366
chr3152974153132E07044748
chr3153343153416E07045117
chr3104810105451E071-2775
chr3105525105633E071-2593
chr3114174114280E0715948
chr3114437114799E0716211
chr3114802115003E0716576
chr3115137115254E0716911
chr3141018141128E07132792
chr3141277141526E07133051
chr3105525105633E072-2593
chr3114174114280E0725948
chr3114437114799E0726211
chr3114802115003E0726576
chr3115137115254E0726911
chr3115361115440E0727135
chr3141018141128E07232792
chr3141018141128E07332792
chr3141277141526E07333051
chr3142138142206E07333912
chr3111467111643E0743241
chr3114437114799E0746211
chr3114802115003E0746576
chr3115137115254E0746911
chr3115361115440E0747135
chr3141018141128E07432792
chr3141277141526E07433051
chr38431584369E081-23857
chr38610586168E081-22058
chr3104810105451E081-2775
chr3105525105633E081-2593
chr3114437114799E0816211
chr3114802115003E0816576
chr3115137115254E0816911
chr3115361115440E0817135
chr3123630123786E08115404
chr3139183139333E08130957
chr3139390139586E08131164
chr3139704139834E08131478
chr3141018141128E08132792
chr3141277141526E08133051
chr38431584369E082-23857
chr3104810105451E082-2775
chr3105525105633E082-2593
chr3114437114799E0826211
chr3114802115003E0826576
chr3115137115254E0826911
chr3115361115440E0827135
chr3117032117204E0828806
chr3117319117416E0829093
chr3117466117544E0829240
chr3139183139333E08230957
chr3139390139586E08231164
chr3139704139834E08231478
chr3141018141128E08232792
chr3141277141526E08233051
chr3142138142206E08233912
chr3152974153132E08244748
chr3153343153416E08245117