rs2416371

Homo sapiens
C>T
KCNN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0146 (4369/29860,GnomAD)
T=0152 (4441/29118,TOPMED)
T=0165 (825/5008,1000G)
T=0176 (679/3854,ALSPAC)
T=0191 (710/3708,TWINSUK)
chr5:114440173 (GRCh38.p7) (5q22.3)
AD
GWASdb2
1   publication(s)
See rs on genome
33 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.114440173C>T
GRCh37.p13 chr 5NC_000005.9:g.113775870C>T

Gene: KCNN2, potassium calcium-activated channel subfamily N member 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
KCNN2 transcript variant 3NM_001278204.1:c.N/AIntron Variant
KCNN2 transcript variant 1NM_021614.3:c.N/AIntron Variant
KCNN2 transcript variant 2NM_170775.2:c.N/AIntron Variant
KCNN2 transcript variant 4NR_103458.1:n.N/AIntron Variant
KCNN2 transcript variant X1XM_011543387.1:c.N/AIntron Variant
KCNN2 transcript variant X2XM_011543389.1:c.N/AIntron Variant
KCNN2 transcript variant X3XM_017009457.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.896T=0.104
1000GenomesAmericanSub694C=0.750T=0.250
1000GenomesEast AsianSub1008C=0.891T=0.109
1000GenomesEuropeSub1006C=0.816T=0.184
1000GenomesGlobalStudy-wide5008C=0.835T=0.165
1000GenomesSouth AsianSub978C=0.780T=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.824T=0.176
The Genome Aggregation DatabaseAfricanSub8700C=0.894T=0.106
The Genome Aggregation DatabaseAmericanSub836C=0.760T=0.240
The Genome Aggregation DatabaseEast AsianSub1616C=0.905T=0.095
The Genome Aggregation DatabaseEuropeSub18408C=0.834T=0.165
The Genome Aggregation DatabaseGlobalStudy-wide29860C=0.853T=0.146
The Genome Aggregation DatabaseOtherSub300C=0.820T=0.180
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.847T=0.152
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.809T=0.191
PMID Title Author Journal
22072270Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.Wang KSJ Neural Transm (Vienna)

P-Value

SNP ID p-value Traits Study
rs24163711.32E-05alcohol withdrawal symptoms22072270

eQTL of rs2416371 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 rs2416371 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 )
chr5113731473113731596E068-44274
chr5113731747113731836E068-44034
chr5113751582113751711E069-24159
chr5113785371113785463E0699501
chr5113785528113786197E0699658
chr5113785176113785314E0709306
chr5113785371113785463E0709501
chr5113785528113786197E0709658
chr5113739160113739230E071-36640
chr5113753362113753443E071-22427
chr5113754006113754141E071-21729
chr5113754463113754654E071-21216
chr5113785528113786197E0719658
chr5113786277113786536E07110407
chr5113785176113785314E0739306
chr5113785371113785463E0739501
chr5113785528113786197E0739658
chr5113773431113773568E081-2302
chr5113773722113774133E081-1737
chr5113774327113774420E081-1450
chr5113775821113775886E0810
chr5113785371113785463E0819501
chr5113785528113786197E0819658
chr5113786277113786536E08110407
chr5113805142113805427E08129272
chr5113773431113773568E082-2302
chr5113773722113774133E082-1737
chr5113774327113774420E082-1450
chr5113785007113785057E0829137
chr5113785176113785314E0829306
chr5113785371113785463E0829501
chr5113785528113786197E0829658
chr5113825103113825237E08249233