rs529989

Homo sapiens
C>A
SYT6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0400 (11948/29854,GnomAD)
C==0427 (12456/29118,TOPMED)
C==0351 (1758/5008,1000G)
C==0435 (1675/3854,ALSPAC)
C==0445 (1651/3708,TWINSUK)
chr1:114135326 (GRCh38.p7) (1p13.2)
ND
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.114135326C>A
GRCh37.p13 chr 1NC_000001.10:g.114677948C>A

Gene: SYT6, synaptotagmin 6(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SYT6 transcript variant 3NM_001270805.1:c.N/AIntron Variant
SYT6 transcript variant 2NM_205848.3:c.N/AIntron Variant
SYT6 transcript variant X5XM_017000371.1:c.N/AIntron Variant
SYT6 transcript variant X6XR_001736985.1:n.N/AIntron Variant
SYT6 transcript variant X1XR_946547.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.406A=0.594
1000GenomesAmericanSub694C=0.320A=0.680
1000GenomesEast AsianSub1008C=0.238A=0.762
1000GenomesEuropeSub1006C=0.437A=0.563
1000GenomesGlobalStudy-wide5008C=0.351A=0.649
1000GenomesSouth AsianSub978C=0.330A=0.670
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.435A=0.565
The Genome Aggregation DatabaseAfricanSub8688C=0.404A=0.596
The Genome Aggregation DatabaseAmericanSub836C=0.290A=0.710
The Genome Aggregation DatabaseEast AsianSub1612C=0.246A=0.754
The Genome Aggregation DatabaseEuropeSub18416C=0.416A=0.583
The Genome Aggregation DatabaseGlobalStudy-wide29854C=0.400A=0.599
The Genome Aggregation DatabaseOtherSub302C=0.460A=0.540
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.427A=0.572
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.445A=0.555
PMID Title Author Journal
23942779A genome-wide association study of behavioral disinhibition.McGue MBehav Genet

P-Value

SNP ID p-value Traits Study
rs5299894.7E-05nicotine use23942779

eQTL of rs529989 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 rs529989 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 )
chr1114646649114646927E068-31021
chr1114657208114657488E068-20460
chr1114665520114666208E068-11740
chr1114657208114657488E069-20460
chr1114664704114664764E069-13184
chr1114660932114661001E070-16947
chr1114661085114661216E070-16732
chr1114690592114690680E07012644
chr1114691499114691549E07013551
chr1114665520114666208E071-11740
chr1114668123114668187E071-9761
chr1114708803114708868E07130855
chr1114708803114708868E07430855
chr1114636781114637191E081-40757
chr1114660584114660874E081-17074
chr1114660932114661001E081-16947
chr1114661085114661216E081-16732
chr1114665309114665425E081-12523
chr1114690592114690680E08112644
chr1114691860114692201E08113912
chr1114692620114692884E08114672
chr1114692620114692884E08214672
chr1114699591114699672E08221643
chr1114699687114699749E08221739







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1114695042114695242E06717094
chr1114695318114695630E06717370
chr1114695665114695966E06717717
chr1114695970114696086E06718022
chr1114696107114696236E06718159
chr1114696288114696393E06718340
chr1114696461114696580E06718513
chr1114694848114694988E06816900
chr1114695042114695242E06817094
chr1114695318114695630E06817370
chr1114695665114695966E06817717
chr1114695970114696086E06818022
chr1114696288114696393E06818340
chr1114696461114696580E06818513
chr1114694848114694988E06916900
chr1114695318114695630E06917370
chr1114695665114695966E06917717
chr1114694220114694295E07016272
chr1114694848114694988E07016900
chr1114695042114695242E07017094
chr1114695318114695630E07017370
chr1114695665114695966E07017717
chr1114694220114694295E07116272
chr1114694848114694988E07116900
chr1114695042114695242E07117094
chr1114695318114695630E07117370
chr1114695042114695242E07217094
chr1114695318114695630E07217370
chr1114695042114695242E07317094
chr1114695318114695630E07317370
chr1114695042114695242E07417094
chr1114695318114695630E07417370
chr1114695665114695966E07417717
chr1114695970114696086E07418022
chr1114696107114696236E07418159
chr1114696288114696393E07418340
chr1114696461114696580E07418513
chr1114693898114693972E08215950
chr1114695042114695242E08217094
chr1114695318114695630E08217370
chr1114695665114695966E08217717
chr1114695970114696086E08218022
chr1114696107114696236E08218159
chr1114696288114696393E08218340
chr1114696461114696580E08218513