rs2454908

Homo sapiens
C>T
ITGAD : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0369 (11033/29894,GnomAD)
C==0323 (9430/29118,TOPMED)
C==0283 (1419/5008,1000G)
C==0436 (1679/3854,ALSPAC)
C==0431 (1598/3708,TWINSUK)
chr16:31399864 (GRCh38.p7) (16p11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
28 Enhancers around
51 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.31399864C>T
GRCh37.p13 chr 16NC_000016.9:g.31411185C>T

Gene: ITGAD, integrin subunit alpha D(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ITGAD transcript variant 1NM_001318185.1:c.N/AIntron Variant
ITGAD transcript variant 2NM_005353.2:c.N/AIntron Variant
ITGAD transcript variant X1XM_011545835.2:c.N/AIntron Variant
ITGAD transcript variant X2XM_011545836.2:c.N/AIntron Variant
ITGAD transcript variant X3XM_011545837.2:c.N/AIntron Variant
ITGAD transcript variant X4XM_011545838.2:c.N/AIntron Variant
ITGAD transcript variant X5XM_011545839.2:c.N/AIntron Variant
ITGAD transcript variant X7XM_011545841.2:c.N/AIntron Variant
ITGAD transcript variant X9XM_011545842.2:c.N/AIntron Variant
ITGAD transcript variant X10XM_011545843.2:c.N/AIntron Variant
ITGAD transcript variant X11XM_011545844.2:c.N/AIntron Variant
ITGAD transcript variant X12XM_011545845.2:c.N/AIntron Variant
ITGAD transcript variant X13XM_011545846.2:c.N/AIntron Variant
ITGAD transcript variant X14XM_011545847.2:c.N/AIntron Variant
ITGAD transcript variant X15XM_011545848.2:c.N/AIntron Variant
ITGAD transcript variant X6XM_017023215.1:c.N/AIntron Variant
ITGAD transcript variant X8XR_950791.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.160T=0.840
1000GenomesAmericanSub694C=0.450T=0.550
1000GenomesEast AsianSub1008C=0.228T=0.772
1000GenomesEuropeSub1006C=0.476T=0.524
1000GenomesGlobalStudy-wide5008C=0.283T=0.717
1000GenomesSouth AsianSub978C=0.190T=0.810
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.436T=0.564
The Genome Aggregation DatabaseAfricanSub8710C=0.183T=0.817
The Genome Aggregation DatabaseAmericanSub836C=0.470T=0.530
The Genome Aggregation DatabaseEast AsianSub1610C=0.248T=0.752
The Genome Aggregation DatabaseEuropeSub18438C=0.460T=0.539
The Genome Aggregation DatabaseGlobalStudy-wide29894C=0.369T=0.630
The Genome Aggregation DatabaseOtherSub300C=0.520T=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.323T=0.676
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.431T=0.569
PMID Title Author Journal
22481050Genetic influences on craving for alcohol.Agrawal AAddict Behav

P-Value

SNP ID p-value Traits Study
rs24549080.00000183alcohol craving with or without dependence22481050
rs24549080.0000404alcohol dependence22481050

eQTL of rs2454908 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr16:31411185TGFB1I1ENSG00000140682.14C>T1.8712e-8-71721Cerebellar_Hemisphere

meQTL of rs2454908 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 )
chr163145191931452495E06740734
chr163143783131438038E06826646
chr163143806731438117E06826882
chr163144006431441007E06828879
chr163145163431451784E06940449
chr163145182131451879E06940636
chr163145191931452495E06940734
chr163145143231451472E07040247
chr163145163431451784E07040449
chr163145182131451879E07040636
chr163145191931452495E07040734
chr163145301431453219E07041829
chr163145182131451879E07140636
chr163145191931452495E07140734
chr163145301431453219E07141829
chr163145191931452495E07240734
chr163145301431453219E07241829
chr163145301431453219E07341829
chr163145191931452495E07440734
chr163143758631437807E08126401
chr163143783131438038E08126646
chr163144006431441007E08128879
chr163145091131451047E08139726
chr163145143231451472E08140247
chr163145163431451784E08140449
chr163145182131451879E08140636
chr163145191931452495E08140734
chr163145301431453219E08141829









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr163143856031439293E06727375
chr163143933331439530E06728148
chr163143957931439953E06728394
chr163145379231453879E06742607
chr163145390331454962E06742718
chr163143856031439293E06827375
chr163143933331439530E06828148
chr163143957931439953E06828394
chr163145367131453738E06842486
chr163145379231453879E06842607
chr163145390331454962E06842718
chr163143856031439293E06927375
chr163143933331439530E06928148
chr163143957931439953E06928394
chr163145379231453879E06942607
chr163145390331454962E06942718
chr163143856031439293E07027375
chr163143933331439530E07028148
chr163143957931439953E07028394
chr163145367131453738E07042486
chr163145379231453879E07042607
chr163145390331454962E07042718
chr163143856031439293E07127375
chr163143933331439530E07128148
chr163143957931439953E07128394
chr163145367131453738E07142486
chr163145379231453879E07142607
chr163145390331454962E07142718
chr163141547131415511E0724286
chr163143856031439293E07227375
chr163143933331439530E07228148
chr163143957931439953E07228394
chr163145367131453738E07242486
chr163145379231453879E07242607
chr163145390331454962E07242718
chr163143856031439293E07327375
chr163143933331439530E07328148
chr163143957931439953E07328394
chr163145367131453738E07342486
chr163145379231453879E07342607
chr163145390331454962E07342718
chr163143856031439293E07427375
chr163143933331439530E07428148
chr163145379231453879E07442607
chr163145390331454962E07442718
chr163143856031439293E08227375
chr163143933331439530E08228148
chr163143957931439953E08228394
chr163145367131453738E08242486
chr163145379231453879E08242607
chr163145390331454962E08242718