rs6141509

Homo sapiens
G>A
NCOA6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0444 (13310/29916,GnomAD)
A=0456 (13296/29118,TOPMED)
A=0451 (2257/5008,1000G)
A=0450 (1735/3854,ALSPAC)
A=0444 (1648/3708,TWINSUK)
chr20:34731584 (GRCh38.p7) (20q11.22)
AD
GWASdb2
1   publication(s)
See rs on genome
98 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.34731584G>A
GRCh37.p13 chr 20NC_000020.10:g.33319388G>A

Gene: NCOA6, nuclear receptor coactivator 6(minus strand)

Molecule type Change Amino acid[Codon] SO Term
NCOA6 transcript variant 2NM_001242539.2:c.N/AIntron Variant
NCOA6 transcript variant 3NM_001318240.1:c.N/AIntron Variant
NCOA6 transcript variant 1NM_014071.4:c.N/AIntron Variant
NCOA6 transcript variant X5XM_011528721.2:c.N/AIntron Variant
NCOA6 transcript variant X7XM_011528726.2:c.N/AIntron Variant
NCOA6 transcript variant X8XM_011528727.2:c.N/AIntron Variant
NCOA6 transcript variant X1XM_017027739.1:c.N/AIntron Variant
NCOA6 transcript variant X2XM_017027740.1:c.N/AIntron Variant
NCOA6 transcript variant X3XM_017027741.1:c.N/AIntron Variant
NCOA6 transcript variant X4XM_017027742.1:c.N/AIntron Variant
NCOA6 transcript variant X6XM_017027743.1:c.N/AIntron Variant
NCOA6 transcript variant X9XM_017027744.1:c.N/AIntron Variant
NCOA6 transcript variant X10XM_017027745.1:c.N/AIntron Variant
NCOA6 transcript variant X13XM_017027747.1:c.N/AIntron Variant
NCOA6 transcript variant X15XM_017027748.1:c.N/AIntron Variant
NCOA6 transcript variant X16XM_017027749.1:c.N/AIntron Variant
NCOA6 transcript variant X18XM_017027750.1:c.N/AIntron Variant
NCOA6 transcript variant X19XM_017027751.1:c.N/AIntron Variant
NCOA6 transcript variant X12XM_006723755.3:c.N/AGenic Downstream Transcript Variant
NCOA6 transcript variant X11XM_017027746.1:c.N/AGenic Downstream Transcript Variant
NCOA6 transcript variant X14XR_001754214.1:n.N/AIntron Variant
NCOA6 transcript variant X17XR_001754215.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.592A=0.408
1000GenomesAmericanSub694G=0.330A=0.670
1000GenomesEast AsianSub1008G=0.487A=0.513
1000GenomesEuropeSub1006G=0.523A=0.477
1000GenomesGlobalStudy-wide5008G=0.549A=0.451
1000GenomesSouth AsianSub978G=0.740A=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.550A=0.450
The Genome Aggregation DatabaseAfricanSub8702G=0.590A=0.410
The Genome Aggregation DatabaseAmericanSub838G=0.280A=0.720
The Genome Aggregation DatabaseEast AsianSub1620G=0.476A=0.524
The Genome Aggregation DatabaseEuropeSub18454G=0.558A=0.442
The Genome Aggregation DatabaseGlobalStudy-wide29916G=0.555A=0.444
The Genome Aggregation DatabaseOtherSub302G=0.550A=0.450
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.543A=0.456
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.556A=0.444
PMID Title Author Journal
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs61415098.8E-07alcohol dependence23089632

eQTL of rs6141509 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr20:33319388MAP1LC3AENSG00000101460.8G>A7.8389e-21184730Cerebellum
Chr20:33319388ACSS2ENSG00000131069.15G>A9.5705e-8-140561Cerebellum
Chr20:33319388MAP1LC3AENSG00000101460.8G>A3.1341e-5184730Frontal_Cortex_BA9
Chr20:33319388MAP1LC3AENSG00000101460.8G>A1.0998e-10184730Cortex
Chr20:33319388ACSS2ENSG00000131069.15G>A4.4982e-5-140561Caudate_basal_ganglia
Chr20:33319388MAP1LC3AENSG00000101460.8G>A5.4946e-5184730Anterior_cingulate_cortex

meQTL of rs6141509 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 )
chr203329077433290844E067-28544
chr203329389533294075E067-25313
chr203329414433294240E067-25148
chr203329424333294405E067-24983
chr203329440633294735E067-24653
chr203329475133294846E067-24542
chr203330074333301764E067-17624
chr203330179133301862E067-17526
chr203330821733308332E067-11056
chr203330882133308976E067-10412
chr203330898033309030E067-10358
chr203332377233324550E0674384
chr203335746233357912E06738074
chr203328129333281524E068-37864
chr203329389533294075E068-25313
chr203329414433294240E068-25148
chr203329424333294405E068-24983
chr203329583633295997E068-23391
chr203329605433296106E068-23282
chr203329614733296256E068-23132
chr203330821733308332E068-11056
chr203330882133308976E068-10412
chr203329389533294075E069-25313
chr203329414433294240E069-25148
chr203329424333294405E069-24983
chr203330821733308332E069-11056
chr203334610133346164E06926713
chr203329389533294075E070-25313
chr203329414433294240E070-25148
chr203329424333294405E070-24983
chr203329440633294735E070-24653
chr203329475133294846E070-24542
chr203329489733295356E070-24032
chr203329539233295501E070-23887
chr203329583633295997E070-23391
chr203329605433296106E070-23282
chr203329614733296256E070-23132
chr203330179133301862E070-17526
chr203330882133308976E070-10412
chr203330898033309030E070-10358
chr203330909733309203E070-10185
chr203328129333281524E071-37864
chr203329389533294075E071-25313
chr203329414433294240E071-25148
chr203329424333294405E071-24983
chr203329440633294735E071-24653
chr203329475133294846E071-24542
chr203329489733295356E071-24032
chr203329583633295997E071-23391
chr203329605433296106E071-23282
chr203329614733296256E071-23132
chr203330179133301862E071-17526
chr203330821733308332E071-11056
chr203330882133308976E071-10412
chr203330898033309030E071-10358
chr203332377233324550E0714384
chr203329389533294075E072-25313
chr203329475133294846E072-24542
chr203329489733295356E072-24032
chr203330821733308332E072-11056
chr203330882133308976E072-10412
chr203330898033309030E072-10358
chr203332377233324550E0724384
chr203329389533294075E073-25313
chr203329414433294240E073-25148
chr203329424333294405E073-24983
chr203329440633294735E073-24653
chr203328129333281524E074-37864
chr203329389533294075E074-25313
chr203329414433294240E074-25148
chr203329424333294405E074-24983
chr203329440633294735E074-24653
chr203329475133294846E074-24542
chr203329489733295356E074-24032
chr203330179133301862E074-17526
chr203330750333307627E074-11761
chr203330763133307864E074-11524
chr203330821733308332E074-11056
chr203329389533294075E081-25313
chr203329414433294240E081-25148
chr203329424333294405E081-24983
chr203329440633294735E081-24653
chr203329475133294846E081-24542
chr203329489733295356E081-24032
chr203329539233295501E081-23887
chr203329583633295997E081-23391
chr203329605433296106E081-23282
chr203329614733296256E081-23132
chr203330074333301764E081-17624
chr203330179133301862E081-17526
chr203332377233324550E0814384
chr203329389533294075E082-25313
chr203329414433294240E082-25148
chr203329424333294405E082-24983
chr203329440633294735E082-24653
chr203330074333301764E082-17624
chr203330179133301862E082-17526
chr203330821733308332E082-11056










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr203329086433293873E067-25515
chr203329627533299370E067-20018
chr203329086433293873E068-25515
chr203329627533299370E068-20018
chr203329086433293873E069-25515
chr203329627533299370E069-20018
chr203329086433293873E070-25515
chr203329627533299370E070-20018
chr203329086433293873E071-25515
chr203329627533299370E071-20018
chr203329086433293873E072-25515
chr203329627533299370E072-20018
chr203329086433293873E073-25515
chr203329627533299370E073-20018
chr203329086433293873E074-25515
chr203329627533299370E074-20018
chr203329086433293873E081-25515
chr203329086433293873E082-25515
chr203329627533299370E082-20018