rs4770875

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ATP8A2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0364 (10905/29944,GnomAD)
G=0394 (11493/29116,TOPMED)
G=0441 (2207/5008,1000G)
G=0304 (1173/3854,ALSPAC)
G=0291 (1080/3708,TWINSUK)

Position: chr13:25745589 (GRCh38.p7) (13q12.13)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 59 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.25745589A>G
ATP8A2 RefSeqGene	NG_042855.1:g.378579A>G
GRCh38.p7 chr 13 alt locus HSCHR13_1_CTG2	NT_187593.1:g.87079T>C
GRCh37.p13 chr 13	NC_000013.10:g.26319727A>G

Gene: ATP8A2, ATPase phospholipid transporting 8A2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP8A2 transcript variant 2	NM_001313741.1:c.	N/A	Intron Variant
ATP8A2 transcript variant 1	NM_016529.5:c.	N/A	Intron Variant
ATP8A2 transcript variant X2	XM_005266419.1:c.	N/A	Intron Variant
ATP8A2 transcript variant X1	XM_011535103.1:c.	N/A	Intron Variant
ATP8A2 transcript variant X3	XM_011535104.2:c.	N/A	Intron Variant
ATP8A2 transcript variant X4	XM_011535106.1:c.	N/A	Intron Variant
ATP8A2 transcript variant X5	XM_011535107.2:c.	N/A	Intron Variant
ATP8A2 transcript variant X6	XM_011535109.2:c.	N/A	Intron Variant
ATP8A2 transcript variant X7	XM_011535112.1:c.	N/A	Intron Variant
ATP8A2 transcript variant X8	XM_011535113.2:c.	N/A	Genic Downstream Transcript Variant
ATP8A2 transcript variant X9	XM_017020625.1:c.	N/A	Genic Downstream Transcript Variant
ATP8A2 transcript variant X10	XM_017020626.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.493	G=0.507
1000Genomes	American	Sub	694	A=0.480	G=0.520
1000Genomes	East Asian	Sub	1008	A=0.509	G=0.491
1000Genomes	Europe	Sub	1006	A=0.714	G=0.286
1000Genomes	Global	Study-wide	5008	A=0.559	G=0.441
1000Genomes	South Asian	Sub	978	A=0.600	G=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.696	G=0.304
The Genome Aggregation Database	African	Sub	8712	A=0.535	G=0.465
The Genome Aggregation Database	American	Sub	836	A=0.490	G=0.510
The Genome Aggregation Database	East Asian	Sub	1618	A=0.512	G=0.488
The Genome Aggregation Database	Europe	Sub	18476	A=0.701	G=0.298
The Genome Aggregation Database	Global	Study-wide	29944	A=0.635	G=0.364
The Genome Aggregation Database	Other	Sub	302	A=0.620	G=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.605	G=0.394
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.709	G=0.291

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4770875	0.000161	nicotine smoking	19268276

eQTL of rs4770875 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 rs4770875 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 )
chr13	26330195	26330235	E068	10468
chr13	26330576	26330940	E068	10849
chr13	26350799	26351221	E068	31072
chr13	26351418	26351469	E068	31691
chr13	26281791	26281855	E070	-37872
chr13	26281949	26282160	E070	-37567
chr13	26282209	26282300	E070	-37427
chr13	26301039	26301102	E070	-18625
chr13	26301231	26301281	E070	-18446
chr13	26301296	26301362	E070	-18365
chr13	26301479	26301758	E070	-17969
chr13	26311586	26311636	E070	-8091
chr13	26312094	26313567	E070	-6160
chr13	26352183	26352308	E070	32456
chr13	26352314	26352844	E070	32587
chr13	26327229	26328830	E071	7502
chr13	26281949	26282160	E081	-37567
chr13	26282209	26282300	E081	-37427
chr13	26305778	26306350	E081	-13377
chr13	26312094	26313567	E081	-6160
chr13	26317680	26317897	E081	-1830
chr13	26317925	26318064	E081	-1663
chr13	26318206	26318277	E081	-1450
chr13	26318355	26318694	E081	-1033
chr13	26318773	26319032	E081	-695
chr13	26319394	26319565	E081	-162
chr13	26319908	26320626	E081	181
chr13	26320727	26320897	E081	1000
chr13	26320917	26321170	E081	1190
chr13	26321390	26321455	E081	1663
chr13	26321670	26321807	E081	1943
chr13	26321959	26322014	E081	2232
chr13	26322702	26322914	E081	2975
chr13	26323241	26323324	E081	3514
chr13	26323362	26323440	E081	3635
chr13	26331194	26331360	E081	11467
chr13	26331477	26331604	E081	11750
chr13	26331627	26331782	E081	11900
chr13	26342593	26343965	E081	22866
chr13	26352116	26352178	E081	32389
chr13	26352183	26352308	E081	32456
chr13	26352314	26352844	E081	32587
chr13	26352916	26354189	E081	33189
chr13	26354760	26354810	E081	35033
chr13	26305597	26305667	E082	-14060
chr13	26305778	26306350	E082	-13377
chr13	26317925	26318064	E082	-1663
chr13	26318206	26318277	E082	-1450
chr13	26318355	26318694	E082	-1033
chr13	26319908	26320626	E082	181
chr13	26320727	26320897	E082	1000
chr13	26350226	26350521	E082	30499
chr13	26350642	26350682	E082	30915
chr13	26350799	26351221	E082	31072
chr13	26351418	26351469	E082	31691
chr13	26351775	26351850	E082	32048
chr13	26352116	26352178	E082	32389
chr13	26356161	26356211	E082	36434
chr13	26356283	26356358	E082	36556