rs7021597

Homo sapiens
A>C
LINGO2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0302 (9034/29904,GnomAD)
C=0343 (1720/5008,1000G)
C=0260 (1002/3854,ALSPAC)
C=0280 (1039/3708,TWINSUK)
chr9:28708153 (GRCh38.p7) (9p21.1)
ND
GWASdb2
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.28708153A>C
GRCh37.p13 chr 9NC_000009.11:g.28708151A>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
1000GenomesAfricanSub1322A=0.713C=0.287
1000GenomesAmericanSub694A=0.510C=0.490
1000GenomesEast AsianSub1008A=0.596C=0.404
1000GenomesEuropeSub1006A=0.739C=0.261
1000GenomesGlobalStudy-wide5008A=0.657C=0.343
1000GenomesSouth AsianSub978A=0.660C=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.740C=0.260
The Genome Aggregation DatabaseAfricanSub8706A=0.699C=0.301
The Genome Aggregation DatabaseAmericanSub836A=0.510C=0.490
The Genome Aggregation DatabaseEast AsianSub1598A=0.551C=0.449
The Genome Aggregation DatabaseEuropeSub18464A=0.716C=0.283
The Genome Aggregation DatabaseGlobalStudy-wide29904A=0.697C=0.302
The Genome Aggregation DatabaseOtherSub300A=0.840C=0.160
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.720C=0.280
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs70215970.000738nicotine dependence17158188

eQTL of rs7021597 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 rs7021597 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 )
chr92870746028707968E081-183
chr92870802828708120E081-31
chr92868763928687689E082-20462
chr92868788528688970E082-19181