rs6060038

Homo sapiens
G>A
NCOA6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0456 (13652/29908,GnomAD)
A=0458 (13346/29118,TOPMED)
A=0478 (2392/5008,1000G)
A=0451 (1738/3854,ALSPAC)
A=0444 (1646/3708,TWINSUK)
chr20:34769912 (GRCh38.p7) (20q11.22)
AD
GWASdb2
1   publication(s)
See rs on genome
127 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.34769912G>A
GRCh37.p13 chr 20NC_000020.10:g.33357715G>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 X12XM_006723755.3: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 X11XM_017027746.1: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 X13XM_017027747.1:c.N/AGenic Upstream 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=0.365A=0.635
1000GenomesEuropeSub1006G=0.512A=0.488
1000GenomesGlobalStudy-wide5008G=0.522A=0.478
1000GenomesSouth AsianSub978G=0.740A=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.549A=0.451
The Genome Aggregation DatabaseAfricanSub8696G=0.592A=0.408
The Genome Aggregation DatabaseAmericanSub838G=0.280A=0.720
The Genome Aggregation DatabaseEast AsianSub1618G=0.378A=0.622
The Genome Aggregation DatabaseEuropeSub18454G=0.547A=0.452
The Genome Aggregation DatabaseGlobalStudy-wide29908G=0.543A=0.456
The Genome Aggregation DatabaseOtherSub302G=0.530A=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.541A=0.458
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
rs60600386.88E-07alcohol dependence23089632

eQTL of rs6060038 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr20:33357715MAP1LC3AENSG00000101460.8G>A7.8389e-21223057Cerebellum
Chr20:33357715ACSS2ENSG00000131069.15G>A9.5705e-8-102234Cerebellum
Chr20:33357715MAP1LC3AENSG00000101460.8G>A3.1341e-5223057Frontal_Cortex_BA9
Chr20:33357715MAP1LC3AENSG00000101460.8G>A1.0998e-10223057Cortex
Chr20:33357715ACSS2ENSG00000131069.15G>A4.4982e-5-102234Caudate_basal_ganglia
Chr20:33357715MAP1LC3AENSG00000101460.8G>A5.4946e-5223057Anterior_cingulate_cortex

meQTL of rs6060038 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 )
chr203330821733308332E067-49383
chr203330882133308976E067-48739
chr203330898033309030E067-48685
chr203332377233324550E067-33165
chr203335746233357912E0670
chr203337913533379889E06721420
chr203338594733386280E06728232
chr203338629133386341E06728576
chr203338634233386405E06728627
chr203338658533386635E06728870
chr203340347533403812E06745760
chr203340419333404300E06746478
chr203340504433405101E06747329
chr203340526633405320E06747551
chr203340553433405726E06747819
chr203340586033405910E06748145
chr203340593733405977E06748222
chr203340648233406532E06748767
chr203330821733308332E068-49383
chr203330882133308976E068-48739
chr203337913533379889E06821420
chr203338594733386280E06828232
chr203338629133386341E06828576
chr203338634233386405E06828627
chr203338658533386635E06828870
chr203338675733386918E06829042
chr203340347533403812E06845760
chr203340419333404300E06846478
chr203340504433405101E06847329
chr203340526633405320E06847551
chr203340553433405726E06847819
chr203340586033405910E06848145
chr203340593733405977E06848222
chr203330821733308332E069-49383
chr203334610133346164E069-11551
chr203338557933385712E06927864
chr203338572633385790E06928011
chr203338594733386280E06928232
chr203338629133386341E06928576
chr203338634233386405E06928627
chr203340347533403812E06945760
chr203340419333404300E06946478
chr203340553433405726E06947819
chr203340586033405910E06948145
chr203340593733405977E06948222
chr203340648233406532E06948767
chr203340738133407425E06949666
chr203340749933407694E06949784
chr203330882133308976E070-48739
chr203330898033309030E070-48685
chr203330909733309203E070-48512
chr203340419333404300E07046478
chr203340526633405320E07047551
chr203340553433405726E07047819
chr203340586033405910E07048145
chr203340593733405977E07048222
chr203330821733308332E071-49383
chr203330882133308976E071-48739
chr203330898033309030E071-48685
chr203332377233324550E071-33165
chr203337902733379077E07121312
chr203337913533379889E07121420
chr203338487733385051E07127162
chr203338522033385367E07127505
chr203338557933385712E07127864
chr203338572633385790E07128011
chr203338594733386280E07128232
chr203338629133386341E07128576
chr203338634233386405E07128627
chr203338658533386635E07128870
chr203340347533403812E07145760
chr203340419333404300E07146478
chr203340504433405101E07147329
chr203340526633405320E07147551
chr203340553433405726E07147819
chr203340586033405910E07148145
chr203340593733405977E07148222
chr203340648233406532E07148767
chr203340738133407425E07149666
chr203340749933407694E07149784
chr203330821733308332E072-49383
chr203330882133308976E072-48739
chr203330898033309030E072-48685
chr203332377233324550E072-33165
chr203337902733379077E07221312
chr203337913533379889E07221420
chr203338594733386280E07228232
chr203338629133386341E07228576
chr203338634233386405E07228627
chr203338658533386635E07228870
chr203339998033400042E07242265
chr203340009433400144E07242379
chr203340347533403812E07245760
chr203340419333404300E07246478
chr203340526633405320E07247551
chr203340553433405726E07247819
chr203340738133407425E07249666
chr203340749933407694E07249784
chr203337902733379077E07321312
chr203337913533379889E07321420
chr203340347533403812E07345760
chr203340419333404300E07346478
chr203340553433405726E07347819
chr203340586033405910E07348145
chr203340593733405977E07348222
chr203340648233406532E07348767
chr203330821733308332E074-49383
chr203337902733379077E07421312
chr203337913533379889E07421420
chr203338557933385712E07427864
chr203338572633385790E07428011
chr203338594733386280E07428232
chr203338629133386341E07428576
chr203338634233386405E07428627
chr203340347533403812E07445760
chr203340419333404300E07446478
chr203340504433405101E07447329
chr203340526633405320E07447551
chr203340553433405726E07447819
chr203340586033405910E07448145
chr203340593733405977E07448222
chr203340648233406532E07448767
chr203340738133407425E07449666
chr203340749933407694E07449784
chr203332377233324550E081-33165
chr203340738133407425E08149666
chr203330821733308332E082-49383