rs10499204

Homo sapiens
T>C
ECT2L : Intron Variant
LOC107986650 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0060 (1822/29962,GnomAD)
C=0068 (1984/29118,TOPMED)
C=0092 (461/5008,1000G)
C=0014 (53/3854,ALSPAC)
C=0015 (54/3708,TWINSUK)
chr6:138895289 (GRCh38.p7) (6q24.1)
AD
GWASdb2
1   publication(s)
See rs on genome
10 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.138895289T>C
GRCh37.p13 chr 6NC_000006.11:g.139216426T>C

Gene: ECT2L, epithelial cell transforming 2 like(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ECT2L transcript variant 1NM_001077706.2:c.N/AIntron Variant
ECT2L transcript variant 2NM_001195037.2:c.N/AIntron Variant
ECT2L transcript variant X1XM_006715472.3:c.N/AIntron Variant
ECT2L transcript variant X2XM_011535795.2:c.N/AIntron Variant
ECT2L transcript variant X5XM_011535797.2:c.N/AIntron Variant
ECT2L transcript variant X3XM_017010828.1:c.N/AIntron Variant
ECT2L transcript variant X4XM_017010829.1:c.N/AIntron Variant
ECT2L transcript variant X6XM_017010830.1:c.N/AGenic Downstream Transcript Variant

Gene: LOC107986650, uncharacterized LOC107986650(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107986650 transcriptXR_001744381.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.833C=0.167
1000GenomesAmericanSub694T=0.980C=0.020
1000GenomesEast AsianSub1008T=0.836C=0.164
1000GenomesEuropeSub1006T=0.979C=0.021
1000GenomesGlobalStudy-wide5008T=0.908C=0.092
1000GenomesSouth AsianSub978T=0.960C=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.986C=0.014
The Genome Aggregation DatabaseAfricanSub8718T=0.869C=0.131
The Genome Aggregation DatabaseAmericanSub836T=0.990C=0.010
The Genome Aggregation DatabaseEast AsianSub1620T=0.862C=0.138
The Genome Aggregation DatabaseEuropeSub18488T=0.976C=0.023
The Genome Aggregation DatabaseGlobalStudy-wide29962T=0.939C=0.060
The Genome Aggregation DatabaseOtherSub300T=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.931C=0.068
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.985C=0.015
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs104992040.000593alcohol dependence21314694

eQTL of rs10499204 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 rs10499204 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 )
chr6139265366139265460E06748940
chr6139265636139265853E06749210
chr6139265297139265355E06848871
chr6139265366139265460E06848940
chr6139265636139265853E06849210
chr6139166648139166752E070-49674
chr6139167012139167062E070-49364
chr6139167416139167644E070-48782
chr6139193583139193635E070-22791
chr6139194047139194183E070-22243