rs1909475

Homo sapiens
T>C
SEPSECS-AS1 : 500B Downstream Variant
LOC105374535 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0344 (10287/29846,GnomAD)
T==0376 (10964/29118,TOPMED)
T==0400 (2002/5008,1000G)
T==0272 (1049/3854,ALSPAC)
T==0278 (1032/3708,TWINSUK)
chr4:25198962 (GRCh38.p7) (4p15.2)
AD
GWASdb2
1   publication(s)
See rs on genome
23 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.25198962T>C
GRCh37.p13 chr 4NC_000004.11:g.25200584T>C

Gene: SEPSECS-AS1, SEPSECS antisense RNA 1 (head to head)(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
SEPSECS-AS1 transcriptNR_037934.1:n.N/ADownstream Transcript Variant

Gene: LOC105374535, uncharacterized LOC105374535(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374535 transcript variant X2XR_001741626.1:n.N/AIntron Variant
LOC105374535 transcript variant X4XR_001741627.1:n.N/AIntron Variant
LOC105374535 transcript variant X6XR_001741629.1:n.N/AIntron Variant
LOC105374535 transcript variant X3XR_925490.2:n.N/AIntron Variant
LOC105374535 transcript variant X1XR_925492.2:n.N/AIntron Variant
LOC105374535 transcript variant X5XR_001741628.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.516C=0.484
1000GenomesAmericanSub694T=0.340C=0.660
1000GenomesEast AsianSub1008T=0.468C=0.532
1000GenomesEuropeSub1006T=0.301C=0.699
1000GenomesGlobalStudy-wide5008T=0.400C=0.600
1000GenomesSouth AsianSub978T=0.320C=0.680
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.272C=0.728
The Genome Aggregation DatabaseAfricanSub8680T=0.483C=0.517
The Genome Aggregation DatabaseAmericanSub836T=0.310C=0.690
The Genome Aggregation DatabaseEast AsianSub1596T=0.449C=0.551
The Genome Aggregation DatabaseEuropeSub18432T=0.273C=0.726
The Genome Aggregation DatabaseGlobalStudy-wide29846T=0.344C=0.655
The Genome Aggregation DatabaseOtherSub302T=0.260C=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.376C=0.623
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.278C=0.722
PMID Title Author Journal
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
rs19094750.000135alcohol dependence21314694

eQTL of rs1909475 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 rs1909475 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 )
chr42516373025163780E067-36804
chr42516381225163862E067-36722
chr42516392525163975E067-36609
chr42517446725175702E067-24882
chr42517640825176621E067-23963
chr42516373025163780E068-36804
chr42516381225163862E068-36722
chr42516392525163975E068-36609
chr42516373025163780E069-36804
chr42517446725175702E069-24882
chr42516373025163780E071-36804
chr42516381225163862E071-36722
chr42516392525163975E071-36609
chr42517446725175702E071-24882
chr42516373025163780E072-36804
chr42516381225163862E072-36722
chr42516392525163975E072-36609
chr42516522625165280E072-35304
chr42517446725175702E072-24882
chr42516373025163780E073-36804
chr42516381225163862E073-36722
chr42516392525163975E073-36609
chr42516373025163780E074-36804







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr42516085825161178E067-39406
chr42516131725163565E067-37019
chr42523499725235047E06734413
chr42523512825237336E06734544
chr42516131725163565E068-37019
chr42523512825237336E06834544
chr42516131725163565E069-37019
chr42523499725235047E06934413
chr42523512825237336E06934544
chr42516085825161178E070-39406
chr42516131725163565E070-37019
chr42523512825237336E07034544
chr42516085825161178E071-39406
chr42516131725163565E071-37019
chr42523512825237336E07134544
chr42516131725163565E072-37019
chr42523499725235047E07234413
chr42523512825237336E07234544
chr42516085825161178E073-39406
chr42516131725163565E073-37019
chr42523499725235047E07334413
chr42523512825237336E07334544
chr42516085825161178E074-39406
chr42516131725163565E074-37019
chr42523499725235047E07434413
chr42523512825237336E07434544
chr42516085825161178E082-39406
chr42516131725163565E082-37019
chr42523512825237336E08234544