rs12348435

Homo sapiens
A>C
LINGO2 : Intron Variant
LOC105376004 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0079 (2375/29922,GnomAD)
C=0104 (3052/29116,TOPMED)
C=0085 (427/5008,1000G)
C=0048 (184/3854,ALSPAC)
C=0056 (209/3708,TWINSUK)
chr9:28600144 (GRCh38.p7) (9p21.1)
AD
GWASdb2 | GWASCatalog
1   publication(s)
See rs on genome
39 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.28600144A>C
GRCh37.p13 chr 9NC_000009.11:g.28600142A>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

Gene: LOC105376004, uncharacterized LOC105376004(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105376004 transcript variant X1XR_001746641.1:n....XR_001746641.1:n.2106A>CA>CNon Coding Transcript Variant
LOC105376004 transcript variant X2XR_929534.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.810C=0.190
1000GenomesAmericanSub694A=0.940C=0.060
1000GenomesEast AsianSub1008A=0.962C=0.038
1000GenomesEuropeSub1006A=0.942C=0.058
1000GenomesGlobalStudy-wide5008A=0.915C=0.085
1000GenomesSouth AsianSub978A=0.960C=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.952C=0.048
The Genome Aggregation DatabaseAfricanSub8712A=0.841C=0.159
The Genome Aggregation DatabaseAmericanSub838A=0.950C=0.050
The Genome Aggregation DatabaseEast AsianSub1610A=0.973C=0.027
The Genome Aggregation DatabaseEuropeSub18460A=0.951C=0.048
The Genome Aggregation DatabaseGlobalStudy-wide29922A=0.920C=0.079
The Genome Aggregation DatabaseOtherSub302A=0.960C=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.895C=0.104
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.944C=0.056
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs123484352E-06alcohol dependence (age at onset)24962325

eQTL of rs12348435 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 rs12348435 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 )
chr92856335728563890E067-36252
chr92859848828598755E067-1387
chr92859883428598942E067-1200
chr92859896828599094E067-1048
chr92859910028599299E067-843
chr92860004728600170E0670
chr92860021028600634E06768
chr92860069628600780E067554
chr92860079528600835E067653
chr92860109228601325E067950
chr92856335728563890E069-36252
chr92859710228597684E069-2458
chr92859830328598375E069-1767
chr92859848828598755E069-1387
chr92859883428598942E069-1200
chr92859896828599094E069-1048
chr92859910028599299E069-843
chr92859830328598375E070-1767
chr92860004728600170E0700
chr92860021028600634E07068
chr92860069628600780E070554
chr92860079528600835E070653
chr92860109228601325E070950
chr92860144228601609E0701300
chr92860221628602266E0702074
chr92860258728602672E0702445
chr92860273628603213E0702594
chr92856335728563890E071-36252
chr92859848828598755E071-1387
chr92860021028600634E07168
chr92860069628600780E071554
chr92860079528600835E071653
chr92860109228601325E071950
chr92860144228601609E0711300
chr92860221628602266E0712074
chr92860258728602672E0712445
chr92859848828598755E072-1387
chr92856310228563191E081-36951
chr92860144228601609E0821300