rs7865532

Homo sapiens
T>C
LINGO2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0337 (10082/29876,GnomAD)
C=0373 (10884/29118,TOPMED)
C=0470 (2356/5008,1000G)
C=0246 (947/3854,ALSPAC)
C=0237 (880/3708,TWINSUK)
chr9:28407494 (GRCh38.p7) (9p21.1)
AD
GWASCatalog
1   publication(s)
See rs on genome
4 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.28407494T>C
GRCh37.p13 chr 9NC_000009.11:g.28407492T>C

Gene: LINGO2, leucine rich repeat and Ig domain containing 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINGO2 transcript variant 2NM_001258282.1:c.N/AIntron Variant
LINGO2 transcript variant 1NM_152570.2:c.N/AIntron Variant
LINGO2 transcript variant X3XM_011517719.1:c.N/AIntron Variant
LINGO2 transcript variant X2XM_017014303.1:c.N/AIntron Variant
LINGO2 transcript variant X6XM_011517724.2:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X7XM_011517728.2:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X3XM_017014304.1:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X4XM_017014305.1:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X6XM_017014306.1:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X8XM_017014307.1:c.N/AGenic Upstream Transcript Variant
LINGO2 transcript variant X1XR_001746186.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.538C=0.462
1000GenomesAmericanSub694T=0.670C=0.330
1000GenomesEast AsianSub1008T=0.293C=0.707
1000GenomesEuropeSub1006T=0.740C=0.260
1000GenomesGlobalStudy-wide5008T=0.530C=0.470
1000GenomesSouth AsianSub978T=0.440C=0.560
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.754C=0.246
The Genome Aggregation DatabaseAfricanSub8704T=0.562C=0.438
The Genome Aggregation DatabaseAmericanSub838T=0.660C=0.340
The Genome Aggregation DatabaseEast AsianSub1586T=0.276C=0.724
The Genome Aggregation DatabaseEuropeSub18446T=0.740C=0.259
The Genome Aggregation DatabaseGlobalStudy-wide29876T=0.662C=0.337
The Genome Aggregation DatabaseOtherSub302T=0.800C=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.626C=0.373
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.763C=0.237
PMID Title Author Journal
24166409Genome-wide association study of alcohol dependence:significant findings in African- and European-Americans including novel risk loci.Gelernter JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs78655324.00E-07alcohol dependence24166409
rs78655322.00E-06alcohol dependence24166409

eQTL of rs7865532 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 rs7865532 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 )
chr92836515728365709E067-41783
chr92844654028446590E07039048
chr92844681328447009E07039321
chr92840740928407684E0810