rs10201643

Homo sapiens
T>G
LYPD6B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0493 (14755/29906,GnomAD)
G=0436 (12701/29118,TOPMED)
G=0428 (2141/5008,1000G)
T==0400 (1543/3854,ALSPAC)
T==0390 (1446/3708,TWINSUK)
chr2:149049127 (GRCh38.p7) (2q23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
64 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.149049127T>G
GRCh37.p13 chr 2NC_000002.11:g.149905641T>G

Gene: LYPD6B, LY6/PLAUR domain containing 6B(plus strand)

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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.821G=0.179
1000GenomesAmericanSub694T=0.430G=0.570
1000GenomesEast AsianSub1008T=0.704G=0.296
1000GenomesEuropeSub1006T=0.386G=0.614
1000GenomesGlobalStudy-wide5008T=0.572G=0.428
1000GenomesSouth AsianSub978T=0.390G=0.610
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.400G=0.600
The Genome Aggregation DatabaseAfricanSub8704T=0.763G=0.237
The Genome Aggregation DatabaseAmericanSub836T=0.440G=0.560
The Genome Aggregation DatabaseEast AsianSub1616T=0.752G=0.248
The Genome Aggregation DatabaseEuropeSub18448T=0.369G=0.630
The Genome Aggregation DatabaseGlobalStudy-wide29906T=0.506G=0.493
The Genome Aggregation DatabaseOtherSub302T=0.410G=0.590
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.563G=0.436
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.390G=0.610
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
rs102016430.0000196alcoholismpha002893
rs102016430.00002alcohol dependence20201924

eQTL of rs10201643 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 rs10201643 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 )
chr2149855746149855800E067-49841
chr2149855877149856491E067-49150
chr2149856612149856662E067-48979
chr2149856819149856947E067-48694
chr2149873784149874238E067-31403
chr2149855746149855800E068-49841
chr2149855877149856491E068-49150
chr2149856612149856662E068-48979
chr2149856819149856947E068-48694
chr2149857160149857268E068-48373
chr2149873784149874238E068-31403
chr2149855877149856491E069-49150
chr2149856612149856662E069-48979
chr2149856819149856947E069-48694
chr2149857160149857268E069-48373
chr2149858124149858274E069-47367
chr2149859275149859325E069-46316
chr2149873784149874238E069-31403
chr2149874326149874761E069-30880
chr2149855746149855800E070-49841
chr2149855877149856491E070-49150
chr2149884133149884705E070-20936
chr2149884750149884924E070-20717
chr2149855746149855800E071-49841
chr2149855877149856491E071-49150
chr2149856612149856662E071-48979
chr2149856819149856947E071-48694
chr2149857160149857268E071-48373
chr2149858124149858274E071-47367
chr2149873784149874238E071-31403
chr2149878345149878523E071-27118
chr2149855746149855800E072-49841
chr2149855877149856491E072-49150
chr2149856612149856662E072-48979
chr2149856819149856947E072-48694
chr2149857160149857268E072-48373
chr2149858124149858274E072-47367
chr2149859275149859325E072-46316
chr2149873784149874238E072-31403
chr2149855746149855800E073-49841
chr2149855877149856491E073-49150
chr2149856612149856662E073-48979
chr2149856819149856947E073-48694
chr2149858124149858274E073-47367
chr2149859275149859325E073-46316
chr2149862077149862614E073-43027
chr2149873784149874238E073-31403
chr2149855746149855800E074-49841
chr2149855877149856491E074-49150
chr2149856612149856662E074-48979
chr2149856819149856947E074-48694
chr2149857160149857268E074-48373
chr2149858124149858274E074-47367
chr2149878345149878523E074-27118
chr2149855746149855800E081-49841
chr2149855877149856491E081-49150
chr2149856612149856662E081-48979
chr2149856819149856947E081-48694
chr2149858124149858274E081-47367
chr2149859275149859325E081-46316
chr2149855746149855800E082-49841
chr2149855877149856491E082-49150
chr2149856612149856662E082-48979
chr2149856819149856947E082-48694










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2149895682149895807E067-9834
chr2149894497149895676E069-9965
chr2149895682149895807E069-9834
chr2149894497149895676E070-9965
chr2149895682149895807E070-9834
chr2149894497149895676E071-9965
chr2149894497149895676E072-9965
chr2149894497149895676E073-9965
chr2149894497149895676E082-9965
chr2149895682149895807E082-9834