rs1197905

Homo sapiens
T>C
LGSN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0470 (14075/29922,GnomAD)
T==0392 (11440/29118,TOPMED)
T==0432 (2165/5008,1000G)
C=0448 (1727/3854,ALSPAC)
C=0450 (1669/3708,TWINSUK)
chr6:63525101 (GRCh38.p7) (6q12)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.63525101T>C
GRCh37.p13 chr 6NC_000006.11:g.64235006T>C

Gene: LGSN, lengsin, lens protein with glutamine synthetase domain(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LGSN transcript variant 2NM_001143940.1:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant 1NM_016571.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X1XM_017010929.1:c.N/AIntron Variant
LGSN transcript variant X2XM_011535889.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X4XM_011535892.2:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X3XM_017010930.1:c.N/AGenic Upstream Transcript Variant
LGSN transcript variant X5XM_017010931.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.190C=0.810
1000GenomesAmericanSub694T=0.420C=0.580
1000GenomesEast AsianSub1008T=0.548C=0.452
1000GenomesEuropeSub1006T=0.580C=0.420
1000GenomesGlobalStudy-wide5008T=0.432C=0.568
1000GenomesSouth AsianSub978T=0.500C=0.500
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.552C=0.448
The Genome Aggregation DatabaseAfricanSub8714T=0.224C=0.776
The Genome Aggregation DatabaseAmericanSub838T=0.420C=0.580
The Genome Aggregation DatabaseEast AsianSub1614T=0.551C=0.449
The Genome Aggregation DatabaseEuropeSub18458T=0.579C=0.421
The Genome Aggregation DatabaseGlobalStudy-wide29922T=0.470C=0.529
The Genome Aggregation DatabaseOtherSub298T=0.640C=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.392C=0.607
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.550C=0.450
PMID Title Author Journal
22096494A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.Zuo LPLoS One

P-Value

SNP ID p-value Traits Study
rs11979059.1E-06alcohol dependence22096494

eQTL of rs1197905 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64235006LGSNENSG00000146166.12T>C1.9599e-12205124Brain_Spinal_cord_cervical

meQTL of rs1197905 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 )
chr66428097464281053E06845968
chr66426311964263520E08128113
chr66426394364264222E08128937


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr66428120864284581E06746202
chr66428120864284581E06846202
chr66428120864284581E06946202
chr66428120864284581E07046202
chr66428120864284581E07146202
chr66428120864284581E07246202
chr66428120864284581E07346202
chr66428120864284581E07446202
chr66428120864284581E08146202
chr66428120864284581E08246202