rs2400954

Homo sapiens
C>T
PPFIA2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0344 (10286/29854,GnomAD)
C==0352 (10273/29118,TOPMED)
C==0307 (1538/5008,1000G)
C==0394 (1519/3854,ALSPAC)
C==0376 (1396/3708,TWINSUK)
chr12:81539202 (GRCh38.p7) (12q21.31)
AD
GWASCatalog
2   publication(s)
See rs on genome
4 Enhancers around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.81539202C>T
GRCh37.p13 chr 12NC_000012.11:g.81932981C>T

Gene: PPFIA2, PTPRF interacting protein alpha 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PPFIA2 transcript variant 2NM_001220473.2:c.N/AIntron Variant
PPFIA2 transcript variant 3NM_001220474.2:c.N/AIntron Variant
PPFIA2 transcript variant 4NM_001220475.2:c.N/AIntron Variant
PPFIA2 transcript variant 5NM_001220476.2:c.N/AIntron Variant
PPFIA2 transcript variant 6NM_001220477.2:c.N/AIntron Variant
PPFIA2 transcript variant 7NM_001220478.2:c.N/AIntron Variant
PPFIA2 transcript variant 1NM_003625.4:c.N/AIntron Variant
PPFIA2 transcript variant 9NM_001220479.2:c.N/AGenic Upstream Transcript Variant
PPFIA2 transcript variant 10NM_001220480.2:c.N/AGenic Upstream Transcript Variant
PPFIA2 transcript variant 8NM_001282536.1:c.N/AGenic Upstream Transcript Variant
PPFIA2 transcript variant X34XM_006719670.3:c.N/AIntron Variant
PPFIA2 transcript variant X39XM_011538906.2:c.N/AIntron Variant
PPFIA2 transcript variant X40XM_011538907.2:c.N/AIntron Variant
PPFIA2 transcript variant X1XM_017020079.1:c.N/AIntron Variant
PPFIA2 transcript variant X2XM_017020080.1:c.N/AIntron Variant
PPFIA2 transcript variant X3XM_017020081.1:c.N/AIntron Variant
PPFIA2 transcript variant X4XM_017020082.1:c.N/AIntron Variant
PPFIA2 transcript variant X5XM_017020083.1:c.N/AIntron Variant
PPFIA2 transcript variant X6XM_017020084.1:c.N/AIntron Variant
PPFIA2 transcript variant X7XM_017020085.1:c.N/AIntron Variant
PPFIA2 transcript variant X8XM_017020086.1:c.N/AIntron Variant
PPFIA2 transcript variant X9XM_017020087.1:c.N/AIntron Variant
PPFIA2 transcript variant X10XM_017020088.1:c.N/AIntron Variant
PPFIA2 transcript variant X11XM_017020089.1:c.N/AIntron Variant
PPFIA2 transcript variant X12XM_017020090.1:c.N/AIntron Variant
PPFIA2 transcript variant X13XM_017020091.1:c.N/AIntron Variant
PPFIA2 transcript variant X14XM_017020092.1:c.N/AIntron Variant
PPFIA2 transcript variant X15XM_017020093.1:c.N/AIntron Variant
PPFIA2 transcript variant X16XM_017020094.1:c.N/AIntron Variant
PPFIA2 transcript variant X17XM_017020095.1:c.N/AIntron Variant
PPFIA2 transcript variant X18XM_017020096.1:c.N/AIntron Variant
PPFIA2 transcript variant X19XM_017020097.1:c.N/AIntron Variant
PPFIA2 transcript variant X20XM_017020098.1:c.N/AIntron Variant
PPFIA2 transcript variant X21XM_017020099.1:c.N/AIntron Variant
PPFIA2 transcript variant X22XM_017020100.1:c.N/AIntron Variant
PPFIA2 transcript variant X23XM_017020101.1:c.N/AIntron Variant
PPFIA2 transcript variant X24XM_017020102.1:c.N/AIntron Variant
PPFIA2 transcript variant X25XM_017020103.1:c.N/AIntron Variant
PPFIA2 transcript variant X26XM_017020104.1:c.N/AIntron Variant
PPFIA2 transcript variant X27XM_017020105.1:c.N/AIntron Variant
PPFIA2 transcript variant X28XM_017020106.1:c.N/AIntron Variant
PPFIA2 transcript variant X29XM_017020107.1:c.N/AIntron Variant
PPFIA2 transcript variant X30XM_017020108.1:c.N/AIntron Variant
PPFIA2 transcript variant X31XM_017020109.1:c.N/AIntron Variant
PPFIA2 transcript variant X32XM_017020110.1:c.N/AIntron Variant
PPFIA2 transcript variant X33XM_017020111.1:c.N/AIntron Variant
PPFIA2 transcript variant X35XM_017020112.1:c.N/AIntron Variant
PPFIA2 transcript variant X36XM_017020113.1:c.N/AIntron Variant
PPFIA2 transcript variant X37XM_017020114.1:c.N/AIntron Variant
PPFIA2 transcript variant X38XM_017020115.1:c.N/AIntron Variant
PPFIA2 transcript variant X39XM_017020116.1:c.N/AIntron Variant
PPFIA2 transcript variant X40XM_017020117.1:c.N/AIntron Variant
PPFIA2 transcript variant X34XM_017020118.1:c.N/AIntron Variant
PPFIA2 transcript variant X42XM_017020119.1:c.N/AIntron Variant
PPFIA2 transcript variant X43XM_017020120.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.313T=0.687
1000GenomesAmericanSub694C=0.350T=0.650
1000GenomesEast AsianSub1008C=0.235T=0.765
1000GenomesEuropeSub1006C=0.400T=0.600
1000GenomesGlobalStudy-wide5008C=0.307T=0.693
1000GenomesSouth AsianSub978C=0.250T=0.750
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.394T=0.606
The Genome Aggregation DatabaseAfricanSub8692C=0.314T=0.686
The Genome Aggregation DatabaseAmericanSub836C=0.330T=0.670
The Genome Aggregation DatabaseEast AsianSub1580C=0.241T=0.759
The Genome Aggregation DatabaseEuropeSub18446C=0.366T=0.633
The Genome Aggregation DatabaseGlobalStudy-wide29854C=0.344T=0.655
The Genome Aggregation DatabaseOtherSub300C=0.440T=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.352T=0.647
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.376T=0.624
PMID Title Author Journal
26365420The genetics of alcohol dependence: Twin and SNP-based heritability, and genome-wide association study based on AUDIT scores.Mbarek HAm J Med Genet B Neuropsychiatr Genet
20012890A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.Ronald ABehav Genet

P-Value

SNP ID p-value Traits Study
rs24009544E-06alcohol dependence26365420

eQTL of rs2400954 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 rs2400954 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 )
chr128192388381923933E068-9048
chr128195540881955607E08122427
chr128195565881955708E08122677
chr128195577681956079E08122795


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr128191389981914107E068-18874
chr128191420481914266E068-18715
chr128191436881914734E068-18247
chr128191389981914107E071-18874
chr128191420481914266E071-18715
chr128191436881914734E071-18247
chr128191389981914107E072-18874
chr128191420481914266E072-18715
chr128191389981914107E074-18874
chr128191420481914266E074-18715