rs4713039

Homo sapiens
A>G
SYCP2L : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0199 (24018/120654,ExAC)
G=0156 (4681/29960,GnomAD)
G=0119 (3470/29118,TOPMED)
A==0150 (1768/11782,GO-ESP)
G=0196 (982/5008,1000G)
G=0190 (732/3854,ALSPAC)
G=0201 (747/3708,TWINSUK)
chr6:10906023 (GRCh38.p7) (6p24.2)
AD
GWASdb2
2   publication(s)
See rs on genome
0 Enhancer around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.10906023A>G
GRCh37.p13 chr 6NC_000006.11:g.10906256A>G

Gene: SYCP2L, synaptonemal complex protein 2 like(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SYCP2L transcriptNM_001040274.2:c....NM_001040274.2:c.645A>GK [AAA]> K [AAG]Coding Sequence Variant
synaptonemal complex protein 2-likeNP_001035364.2:p....NP_001035364.2:p.Lys215=K [Lys]> K [Lys]Synonymous Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.966G=0.034
1000GenomesAmericanSub694A=0.890G=0.110
1000GenomesEast AsianSub1008A=0.623G=0.377
1000GenomesEuropeSub1006A=0.812G=0.188
1000GenomesGlobalStudy-wide5008A=0.804G=0.196
1000GenomesSouth AsianSub978A=0.700G=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.810G=0.190
The Exome Aggregation ConsortiumAmericanSub21362A=0.920G=0.079
The Exome Aggregation ConsortiumAsianSub25124A=0.676G=0.323
The Exome Aggregation ConsortiumEuropeSub73270A=0.809G=0.191
The Exome Aggregation ConsortiumGlobalStudy-wide120654A=0.800G=0.199
The Exome Aggregation ConsortiumOtherSub898A=0.790G=0.210
The Genome Aggregation DatabaseAfricanSub8726A=0.950G=0.050
The Genome Aggregation DatabaseAmericanSub834A=0.880G=0.120
The Genome Aggregation DatabaseEast AsianSub1608A=0.619G=0.381
The Genome Aggregation DatabaseEuropeSub18490A=0.811G=0.188
The Genome Aggregation DatabaseGlobalStudy-wide29960A=0.843G=0.156
The Genome Aggregation DatabaseOtherSub302A=0.850G=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.880G=0.119
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.799G=0.201
PMID Title Author Journal
26870257Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study.Qu LSOncol Lett
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs47130390.000185alcohol dependence21314694

eQTL of rs4713039 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 rs4713039 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.

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr61088691310887784E067-18472
chr61088691310887784E068-18472
chr61088691310887784E069-18472
chr61088691310887784E071-18472
chr61088675810886820E072-19436
chr61088691310887784E072-18472
chr61088691310887784E073-18472
chr61088691310887784E074-18472
chr61088675810886820E082-19436
chr61088691310887784E082-18472
chr61088781410888141E082-18115