SNP Detail Info-rs2400954

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.81539202C>T
GRCh37.p13 chr 12	NC_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 2	NM_001220473.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 3	NM_001220474.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 4	NM_001220475.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 5	NM_001220476.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 6	NM_001220477.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 7	NM_001220478.2:c.	N/A	Intron Variant
PPFIA2 transcript variant 1	NM_003625.4:c.	N/A	Intron Variant
PPFIA2 transcript variant 9	NM_001220479.2:c.	N/A	Genic Upstream Transcript Variant
PPFIA2 transcript variant 10	NM_001220480.2:c.	N/A	Genic Upstream Transcript Variant
PPFIA2 transcript variant 8	NM_001282536.1:c.	N/A	Genic Upstream Transcript Variant
PPFIA2 transcript variant X34	XM_006719670.3:c.	N/A	Intron Variant
PPFIA2 transcript variant X39	XM_011538906.2:c.	N/A	Intron Variant
PPFIA2 transcript variant X40	XM_011538907.2:c.	N/A	Intron Variant
PPFIA2 transcript variant X1	XM_017020079.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X2	XM_017020080.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X3	XM_017020081.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X4	XM_017020082.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X5	XM_017020083.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X6	XM_017020084.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X7	XM_017020085.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X8	XM_017020086.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X9	XM_017020087.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X10	XM_017020088.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X11	XM_017020089.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X12	XM_017020090.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X13	XM_017020091.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X14	XM_017020092.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X15	XM_017020093.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X16	XM_017020094.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X17	XM_017020095.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X18	XM_017020096.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X19	XM_017020097.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X20	XM_017020098.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X21	XM_017020099.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X22	XM_017020100.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X23	XM_017020101.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X24	XM_017020102.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X25	XM_017020103.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X26	XM_017020104.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X27	XM_017020105.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X28	XM_017020106.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X29	XM_017020107.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X30	XM_017020108.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X31	XM_017020109.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X32	XM_017020110.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X33	XM_017020111.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X35	XM_017020112.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X36	XM_017020113.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X37	XM_017020114.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X38	XM_017020115.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X39	XM_017020116.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X40	XM_017020117.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X34	XM_017020118.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X42	XM_017020119.1:c.	N/A	Intron Variant
PPFIA2 transcript variant X43	XM_017020120.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.313	T=0.687
1000Genomes	American	Sub	694	C=0.350	T=0.650
1000Genomes	East Asian	Sub	1008	C=0.235	T=0.765
1000Genomes	Europe	Sub	1006	C=0.400	T=0.600
1000Genomes	Global	Study-wide	5008	C=0.307	T=0.693
1000Genomes	South Asian	Sub	978	C=0.250	T=0.750
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.394	T=0.606
The Genome Aggregation Database	African	Sub	8692	C=0.314	T=0.686
The Genome Aggregation Database	American	Sub	836	C=0.330	T=0.670
The Genome Aggregation Database	East Asian	Sub	1580	C=0.241	T=0.759
The Genome Aggregation Database	Europe	Sub	18446	C=0.366	T=0.633
The Genome Aggregation Database	Global	Study-wide	29854	C=0.344	T=0.655
The Genome Aggregation Database	Other	Sub	300	C=0.440	T=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.352	T=0.647
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.376	T=0.624

PMID	Title	Author	Journal
26365420	The genetics of alcohol dependence: Twin and SNP-based heritability, and genome-wide association study based on AUDIT scores.	Mbarek H	Am J Med Genet B Neuropsychiatr Genet
20012890	A 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 A	Behav Genet

P-Value

SNP ID	p-value	Traits	Study
rs2400954	4E-06	alcohol dependence	26365420

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr12	81923883	81923933	E068	-9048
chr12	81955408	81955607	E081	22427
chr12	81955658	81955708	E081	22677
chr12	81955776	81956079	E081	22795

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	81913899	81914107	E068	-18874
chr12	81914204	81914266	E068	-18715
chr12	81914368	81914734	E068	-18247
chr12	81913899	81914107	E071	-18874
chr12	81914204	81914266	E071	-18715
chr12	81914368	81914734	E071	-18247
chr12	81913899	81914107	E072	-18874
chr12	81914204	81914266	E072	-18715
chr12	81913899	81914107	E074	-18874
chr12	81914204	81914266	E074	-18715

rs2400954

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs2400954 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2400954 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)