rs10257489

Homo sapiens
A>C / A>G / A>T
AUTS2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0448 (13419/29930,GnomAD)
A==0492 (2465/5008,1000G)
G=0489 (1886/3854,ALSPAC)
G=0493 (1827/3708,TWINSUK)
chr7:70672131 (GRCh38.p7) (7q11.22)
ND
GWASdb2
1   publication(s)
See rs on genome
65 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.70672131A>C
GRCh38.p7 chr 7NC_000007.14:g.70672131A>G
GRCh38.p7 chr 7NC_000007.14:g.70672131A>T
GRCh37.p13 chr 7NC_000007.13:g.70137117A>C
GRCh37.p13 chr 7NC_000007.13:g.70137117A>G
GRCh37.p13 chr 7NC_000007.13:g.70137117A>T
AUTS2 RefSeqGeneNG_034133.1:g.1078213A>C
AUTS2 RefSeqGeneNG_034133.1:g.1078213A>G
AUTS2 RefSeqGeneNG_034133.1:g.1078213A>T

Gene: AUTS2, autism susceptibility candidate 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
AUTS2 transcript variant 2NM_001127231.2:c.N/AIntron Variant
AUTS2 transcript variant 1NM_015570.3:c.N/AIntron Variant
AUTS2 transcript variant 3NM_001127232.2:c.N/AGenic Downstream Transcript Variant
AUTS2 transcript variant X1XM_011516010.2:c.N/AIntron Variant
AUTS2 transcript variant X2XM_011516011.2:c.N/AIntron Variant
AUTS2 transcript variant X3XM_011516012.2:c.N/AIntron Variant
AUTS2 transcript variant X4XM_011516013.2:c.N/AIntron Variant
AUTS2 transcript variant X5XM_011516014.2:c.N/AIntron Variant
AUTS2 transcript variant X6XM_011516017.2:c.N/AIntron Variant
AUTS2 transcript variant X7XM_011516018.2:c.N/AIntron Variant
AUTS2 transcript variant X9XM_017011951.1:c.N/AIntron Variant
AUTS2 transcript variant X8XM_005250257.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.222G=0.778
1000GenomesAmericanSub694A=0.530G=0.470
1000GenomesEast AsianSub1008A=0.686G=0.314
1000GenomesEuropeSub1006A=0.524G=0.476
1000GenomesGlobalStudy-wide5008A=0.492G=0.508
1000GenomesSouth AsianSub978A=0.600G=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.511G=0.489
The Genome Aggregation DatabaseAfricanSub8706A=0.284T=0.000
The Genome Aggregation DatabaseAmericanSub834A=0.520T=0.00,
The Genome Aggregation DatabaseEast AsianSub1610A=0.677T=0.000
The Genome Aggregation DatabaseEuropeSub18478A=0.499T=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29930A=0.448T=0.000
The Genome Aggregation DatabaseOtherSub302A=0.620T=0.00,
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.507G=0.493
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs102574890.000562nicotine smoking19268276

eQTL of rs10257489 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 rs10257489 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 )
chr72525545025255817E068-29012
chr72525584525255930E068-28899
chr72525617425256238E068-28591
chr72529915125299201E06814322
chr72529921825299887E06814389
chr72530007125300177E06815242
chr72530188725301968E06817058
chr72531505125315157E06830222
chr72532809425328268E06843265
chr72532832625328448E06843497
chr72532863425328799E06843805
chr72532890225329002E06844073
chr72532909625329248E06844267
chr72532809425328268E06943265
chr72532832625328448E06943497
chr72532863425328799E06943805
chr72532890225329002E06944073
chr72532909625329248E06944267
chr72532928025329448E06944451
chr72529497025295097E07010141
chr72529516525296318E07010336
chr72529915125299201E07014322
chr72529921825299887E07014389
chr72530007125300177E07015242
chr72530038725300633E07015558
chr72532809425328268E07043265
chr72532832625328448E07043497
chr72532863425328799E07043805
chr72532890225329002E07044073
chr72532909625329248E07044267
chr72533255825332695E07047729
chr72533271825332768E07047889
chr72533283825332878E07048009
chr72533321825333269E07048389
chr72533343825333573E07048609
chr72529915125299201E07114322
chr72529921825299887E07114389
chr72530007125300177E07115242
chr72530038725300633E07115558
chr72529915125299201E07314322
chr72529921825299887E07314389
chr72530007125300177E07315242
chr72532809425328268E07343265
chr72532832625328448E07343497
chr72532863425328799E07343805
chr72532890225329002E07344073
chr72532909625329248E07344267
chr72532928025329448E07344451
chr72529915125299201E07414322
chr72529921825299887E07414389
chr72530038725300633E07415558
chr72528286625282948E081-1881
chr72528331825283416E081-1413
chr72528351725283824E081-1005
chr72529516525296318E08110336
chr72529659325296643E08111764
chr72529915125299201E08114322
chr72529921825299887E08114389
chr72532334625323412E08138517
chr72532352925323579E08138700
chr72532360025323686E08138771
chr72529516525296318E08210336
chr72529659325296643E08211764
chr72530038725300633E08215558
chr72530063725301875E08215808