rs9860340

Homo sapiens
A>C / A>G
LOC105377198 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0392 (11756/29940,GnomAD)
G=0440 (12819/29118,TOPMED)
G=0403 (2019/5008,1000G)
G=0241 (929/3854,ALSPAC)
G=0232 (861/3708,TWINSUK)
chr3:87734826 (GRCh38.p7) (3p11.2)
AD
GWASCatalog
1   publication(s)
See rs on genome
34 Enhancers around
5 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.87734826A>C
GRCh38.p7 chr 3NC_000003.12:g.87734826A>G
GRCh37.p13 chr 3NC_000003.11:g.87783976A>C
GRCh37.p13 chr 3NC_000003.11:g.87783976A>G

Gene: LOC105377198, uncharacterized LOC105377198(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377198 transcriptXR_941033.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.258G=0.742
1000GenomesAmericanSub694A=0.710G=0.290
1000GenomesEast AsianSub1008A=0.564G=0.436
1000GenomesEuropeSub1006A=0.749G=0.251
1000GenomesGlobalStudy-wide5008A=0.597G=0.403
1000GenomesSouth AsianSub978A=0.850G=0.150
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.759G=0.241
The Genome Aggregation DatabaseAfricanSub8712A=0.329C=0.000
The Genome Aggregation DatabaseAmericanSub834A=0.740C=0.00,
The Genome Aggregation DatabaseEast AsianSub1612A=0.591C=0.000
The Genome Aggregation DatabaseEuropeSub18480A=0.731C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29940A=0.607C=0.000
The Genome Aggregation DatabaseOtherSub302A=0.790C=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.559G=0.440
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.768G=0.232
PMID Title Author Journal
22554406Family-based genome-wide association study of frontal theta oscillations identifies potassium channel gene KCNJ6.Kang SJGenes Brain Behav

P-Value

SNP ID p-value Traits Study
rs98603404E-06alcohol dependence22554406

eQTL of rs9860340 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 rs9860340 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 )
chr34520838245208428E06825368
chr34520854945209472E06825535
chr34521160845211994E06828594
chr34518518345185423E0692169
chr34518572845185786E0692714
chr34520948345209656E07026469
chr34521123645211322E07028222
chr34521160845211994E07028594
chr34522925345229514E07046239
chr34523035945230490E07047345
chr34523075045230800E07047736
chr34518044045181435E071-1579
chr34520948345209656E07126469
chr34520838245208428E07325368
chr34520854945209472E07325535
chr34514246345142796E081-40218
chr34514294545143053E081-39961
chr34514586545146094E081-36920
chr34518044045181435E081-1579
chr34518146345181603E081-1411
chr34518161145181908E081-1106
chr34518195845182186E081-828
chr34518238045182430E081-584
chr34520838245208428E08125368
chr34520854945209472E08125535
chr34520948345209656E08126469
chr34523035945230490E08147345
chr34523075045230800E08147736
chr34518044045181435E082-1579
chr34518146345181603E082-1411
chr34518161145181908E082-1106
chr34518195845182186E082-828
chr34518238045182430E082-584
chr34520838245208428E08225368







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr34518660845186774E0683594
chr34518679345188374E0683779
chr34518679345188374E0733779
chr34518679345188374E0743779
chr34518679345188374E0823779