rs2824642

Homo sapiens
C>G / C>T
CHODL : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0382 (11412/29872,GnomAD)
G=0396 (11554/29118,TOPMED)
G=0489 (2451/5008,1000G)
G=0258 (995/3854,ALSPAC)
G=0269 (999/3708,TWINSUK)
chr21:18131787 (GRCh38.p7) (21q21.1)
ND
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.18131787C>G
GRCh38.p7 chr 21NC_000021.9:g.18131787C>T
GRCh37.p13 chr 21NC_000021.8:g.19504104C>G
GRCh37.p13 chr 21NC_000021.8:g.19504104C>T
CHODL RefSeqGeneNG_029478.1:g.219448C>G
CHODL RefSeqGeneNG_029478.1:g.219448C>T

Gene: CHODL, chondrolectin(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CHODL transcript variant 3NM_001204175.1:c.N/AIntron Variant
CHODL transcript variant 4NM_001204176.1:c.N/AIntron Variant
CHODL transcript variant 5NM_001204177.1:c.N/AIntron Variant
CHODL transcript variant 6NM_001204178.1:c.N/AIntron Variant
CHODL transcript variant 2NM_001204174.1:c.N/AGenic Upstream Transcript Variant
CHODL transcript variant 1NM_024944.2:c.N/AGenic Upstream Transcript Variant
CHODL transcript variant X3XM_011529457.2:c.N/AIntron Variant
CHODL transcript variant X2XM_011529453.2:c.N/AGenic Upstream Transcript Variant
CHODL transcript variant X1XM_017028273.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.486G=0.514
1000GenomesAmericanSub694C=0.540G=0.460
1000GenomesEast AsianSub1008C=0.263G=0.737
1000GenomesEuropeSub1006C=0.719G=0.281
1000GenomesGlobalStudy-wide5008C=0.511G=0.489
1000GenomesSouth AsianSub978C=0.560G=0.440
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.742G=0.258
The Genome Aggregation DatabaseAfricanSub8692C=0.496G=0.504
The Genome Aggregation DatabaseAmericanSub834C=0.510G=0.490
The Genome Aggregation DatabaseEast AsianSub1616C=0.263G=0.737
The Genome Aggregation DatabaseEuropeSub18428C=0.711G=0.289
The Genome Aggregation DatabaseGlobalStudy-wide29872C=0.618G=0.382
The Genome Aggregation DatabaseOtherSub302C=0.630G=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.603G=0.396
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.731G=0.269
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs28246420.000171nicotine smoking19268276

eQTL of rs2824642 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 rs2824642 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 )
chr213635253536352620E068-24601
chr213635266136352752E068-24469
chr213635276736352835E068-24386
chr213635289136353077E068-24144
chr213642562336426088E07148402
chr213642613236426204E07148911
chr213642626836426320E07149047
chr213642562336426088E07448402
chr213642613236426204E07448911
chr213642626836426320E07449047
chr213642659236426642E07449371
chr213634175236342065E081-35156
chr213634214636342524E081-34697
chr213634253436342648E081-34573




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr213641915636422031E06841935
chr213641915636422031E06941935
chr213641915636422031E07141935
chr213641915636422031E07441935