rs6475490

Homo sapiens
G>C
FOCAD : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0362 (10839/29946,GnomAD)
G==0373 (10860/29118,TOPMED)
G==0397 (1986/5008,1000G)
G==0320 (1235/3854,ALSPAC)
G==0304 (1126/3708,TWINSUK)
chr9:20945208 (GRCh38.p7) (9p21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
58 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.20945208G>C
GRCh37.p13 chr 9NC_000009.11:g.20945207G>C

Gene: FOCAD, focadhesin(plus strand)

Molecule type Change Amino acid[Codon] SO Term
FOCAD transcriptNM_017794.4:c.N/AIntron Variant
FOCAD transcript variant X7XM_005251494.3:c.N/AIntron Variant
FOCAD transcript variant X7XM_011517945.2:c.N/AIntron Variant
FOCAD transcript variant X1XM_017014852.1:c.N/AIntron Variant
FOCAD transcript variant X2XM_017014853.1:c.N/AIntron Variant
FOCAD transcript variant X3XM_017014854.1:c.N/AIntron Variant
FOCAD transcript variant X4XM_017014855.1:c.N/AIntron Variant
FOCAD transcript variant X5XM_017014856.1:c.N/AIntron Variant
FOCAD transcript variant X8XM_017014857.1:c.N/AIntron Variant
FOCAD transcript variant X9XM_017014858.1:c.N/AIntron Variant
FOCAD transcript variant X12XM_017014859.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.472C=0.528
1000GenomesAmericanSub694G=0.430C=0.570
1000GenomesEast AsianSub1008G=0.469C=0.531
1000GenomesEuropeSub1006G=0.311C=0.689
1000GenomesGlobalStudy-wide5008G=0.397C=0.603
1000GenomesSouth AsianSub978G=0.290C=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.320C=0.680
The Genome Aggregation DatabaseAfricanSub8716G=0.450C=0.550
The Genome Aggregation DatabaseAmericanSub834G=0.440C=0.560
The Genome Aggregation DatabaseEast AsianSub1616G=0.443C=0.557
The Genome Aggregation DatabaseEuropeSub18480G=0.311C=0.688
The Genome Aggregation DatabaseGlobalStudy-wide29946G=0.362C=0.638
The Genome Aggregation DatabaseOtherSub300G=0.260C=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.373C=0.627
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.304C=0.696
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
rs64754900.000984alcohol dependence21314694

eQTL of rs6475490 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 rs6475490 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 )
chr92094098220941472E067-3735
chr92094149620941582E067-3625
chr92094541420945733E067207
chr92094541420945733E068207
chr92099009020990317E06844883
chr92099031920990463E06845112
chr92099061420990664E06845407
chr92099068620990901E06845479
chr92098995420990083E06944747
chr92099009020990317E06944883
chr92099031920990463E06945112
chr92099061420990664E06945407
chr92099068620990901E06945479
chr92099098020991157E06945773
chr92090011520900212E070-44995
chr92090070020900927E070-44280
chr92090110520901155E070-44052
chr92095519320955311E0709986
chr92095538420955513E07010177
chr92099009020990317E07044883
chr92099031920990463E07045112
chr92099061420990664E07045407
chr92099068620990901E07045479
chr92094541420945733E071207
chr92094627320946388E0711066
chr92094672320946826E0711516
chr92099009020990317E07144883
chr92099031920990463E07145112
chr92099061420990664E07145407
chr92099068620990901E07145479
chr92099098020991157E07145773
chr92094541420945733E072207
chr92099031920990463E07245112
chr92099061420990664E07245407
chr92095462320954748E0739416
chr92094541420945733E074207
chr92094627320946388E0741066
chr92094672320946826E0741516
chr92099009020990317E07444883
chr92099031920990463E07445112
chr92099061420990664E07445407
chr92099068620990901E07445479
chr92092843420928488E081-16719
chr92092860320928696E081-16511
chr92092878520928871E081-16336
chr92092983120929881E081-15326
chr92092996920930019E081-15188
chr92093044120931287E081-13920
chr92093158020931630E081-13577
chr92093172520931775E081-13432
chr92093183720931887E081-13320
chr92093229720932424E081-12783
chr92092843420928488E082-16719
chr92092860320928696E082-16511
chr92092878520928871E082-16336
chr92092983120929881E082-15326
chr92092996920930019E082-15188
chr92093044120931287E082-13920