rs16822509

Homo sapiens
T>C
LYPD6B : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0497 (14838/29852,GnomAD)
C=0448 (13057/29118,TOPMED)
C=0437 (2187/5008,1000G)
T==0395 (1524/3854,ALSPAC)
T==0387 (1436/3708,TWINSUK)
chr2:149038210 (GRCh38.p7) (2q23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
110 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.149038210T>C
GRCh37.p13 chr 2NC_000002.11:g.149894724T>C

Gene: LYPD6B, LY6/PLAUR domain containing 6B(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LYPD6B transcript variant 3NM_001317003.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant 5NM_001317005.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant 6NM_001317006.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant 1NM_177964.4:c.N/AUpstream Transcript Variant
LYPD6B transcript variant 2NM_001317002.1:c.N/AN/A
LYPD6B transcript variant 4NM_001317004.1:c.N/AN/A
LYPD6B transcript variant X7XM_011510623.2:c.N/AUpstream Transcript Variant
LYPD6B transcript variant X2XM_017003364.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant X8XM_017003365.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant X9XM_017003366.1:c.N/AUpstream Transcript Variant
LYPD6B transcript variant X3XM_005246306.4:c.N/AN/A
LYPD6B transcript variant X4XM_006712279.2:c.N/AN/A
LYPD6B transcript variant X5XM_006712280.3:c.N/AN/A
LYPD6B transcript variant X6XM_006712281.3:c.N/AN/A
LYPD6B transcript variant X1XM_011510620.2:c.N/AN/A
LYPD6B transcript variant X10XM_011510625.1:c.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.795C=0.205
1000GenomesAmericanSub694T=0.420C=0.580
1000GenomesEast AsianSub1008T=0.708C=0.292
1000GenomesEuropeSub1006T=0.381C=0.619
1000GenomesGlobalStudy-wide5008T=0.563C=0.437
1000GenomesSouth AsianSub978T=0.390C=0.610
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.395C=0.605
The Genome Aggregation DatabaseAfricanSub8688T=0.737C=0.263
The Genome Aggregation DatabaseAmericanSub834T=0.430C=0.570
The Genome Aggregation DatabaseEast AsianSub1610T=0.753C=0.247
The Genome Aggregation DatabaseEuropeSub18418T=0.366C=0.633
The Genome Aggregation DatabaseGlobalStudy-wide29852T=0.497C=0.502
The Genome Aggregation DatabaseOtherSub302T=0.390C=0.610
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.551C=0.448
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.387C=0.613
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs168225090.000032alcohol dependence20201924
rs168225090.0000322alcoholismpha002893

eQTL of rs16822509 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 rs16822509 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 )
chr2149846322149846408E067-48316
chr2149846459149846723E067-48001
chr2149854829149854927E067-39797
chr2149855158149855224E067-39500
chr2149855279149855333E067-39391
chr2149855461149855550E067-39174
chr2149855746149855800E067-38924
chr2149855877149856491E067-38233
chr2149856612149856662E067-38062
chr2149856819149856947E067-37777
chr2149873784149874238E067-20486
chr2149854829149854927E068-39797
chr2149855158149855224E068-39500
chr2149855279149855333E068-39391
chr2149855461149855550E068-39174
chr2149855746149855800E068-38924
chr2149855877149856491E068-38233
chr2149856612149856662E068-38062
chr2149856819149856947E068-37777
chr2149857160149857268E068-37456
chr2149873784149874238E068-20486
chr2149854829149854927E069-39797
chr2149855158149855224E069-39500
chr2149855877149856491E069-38233
chr2149856612149856662E069-38062
chr2149856819149856947E069-37777
chr2149857160149857268E069-37456
chr2149858124149858274E069-36450
chr2149859275149859325E069-35399
chr2149873784149874238E069-20486
chr2149874326149874761E069-19963
chr2149855158149855224E070-39500
chr2149855279149855333E070-39391
chr2149855461149855550E070-39174
chr2149855746149855800E070-38924
chr2149855877149856491E070-38233
chr2149884133149884705E070-10019
chr2149884750149884924E070-9800
chr2149847685149847747E071-46977
chr2149854829149854927E071-39797
chr2149855158149855224E071-39500
chr2149855279149855333E071-39391
chr2149855461149855550E071-39174
chr2149855746149855800E071-38924
chr2149855877149856491E071-38233
chr2149856612149856662E071-38062
chr2149856819149856947E071-37777
chr2149857160149857268E071-37456
chr2149858124149858274E071-36450
chr2149873784149874238E071-20486
chr2149878345149878523E071-16201
chr2149846322149846408E072-48316
chr2149846459149846723E072-48001
chr2149854829149854927E072-39797
chr2149855158149855224E072-39500
chr2149855279149855333E072-39391
chr2149855461149855550E072-39174
chr2149855746149855800E072-38924
chr2149855877149856491E072-38233
chr2149856612149856662E072-38062
chr2149856819149856947E072-37777
chr2149857160149857268E072-37456
chr2149858124149858274E072-36450
chr2149859275149859325E072-35399
chr2149873784149874238E072-20486
chr2149846322149846408E073-48316
chr2149846459149846723E073-48001
chr2149854829149854927E073-39797
chr2149855158149855224E073-39500
chr2149855279149855333E073-39391
chr2149855461149855550E073-39174
chr2149855746149855800E073-38924
chr2149855877149856491E073-38233
chr2149856612149856662E073-38062
chr2149856819149856947E073-37777
chr2149858124149858274E073-36450
chr2149859275149859325E073-35399
chr2149862077149862614E073-32110
chr2149873784149874238E073-20486
chr2149846322149846408E074-48316
chr2149846459149846723E074-48001
chr2149847685149847747E074-46977
chr2149855158149855224E074-39500
chr2149855279149855333E074-39391
chr2149855461149855550E074-39174
chr2149855746149855800E074-38924
chr2149855877149856491E074-38233
chr2149856612149856662E074-38062
chr2149856819149856947E074-37777
chr2149857160149857268E074-37456
chr2149858124149858274E074-36450
chr2149878345149878523E074-16201
chr2149854829149854927E081-39797
chr2149855158149855224E081-39500
chr2149855279149855333E081-39391
chr2149855461149855550E081-39174
chr2149855746149855800E081-38924
chr2149855877149856491E081-38233
chr2149856612149856662E081-38062
chr2149856819149856947E081-37777
chr2149858124149858274E081-36450
chr2149859275149859325E081-35399
chr2149854829149854927E082-39797
chr2149855158149855224E082-39500
chr2149855279149855333E082-39391
chr2149855461149855550E082-39174
chr2149855746149855800E082-38924
chr2149855877149856491E082-38233
chr2149856612149856662E082-38062
chr2149856819149856947E082-37777










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2149895682149895807E067958
chr2149894497149895676E0690
chr2149895682149895807E069958
chr2149894497149895676E0700
chr2149895682149895807E070958
chr2149894497149895676E0710
chr2149894497149895676E0720
chr2149894497149895676E0730
chr2149894497149895676E0820
chr2149895682149895807E082958