chr6:160840252:G>T Detail (hg19) (SLC22A3)

Information

Genome

Assembly Position
hg19 chr6:160,840,252-160,840,252
hg38 chr6:160,419,220-160,419,220 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_021977.3:c.975+8374G>T
Ensemble ENST00000275300.3:c.975+8374G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.240
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 604842 OMIM
HGNC 10967 HGNC
Ensembl ENSG00000146477 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv27707517 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.162 colorectal cancer Moreover, we found cumulative effects of three genetic factors (rs7758229, rs698... BeFree 21242260 Detail
0.009 colorectal carcinoma Moreover, we found cumulative effects of three genetic factors (rs7758229, rs698... BeFree 21242260 Detail
0.124 colorectal cancer Common variant in 6q26-q27 is associated with distal colon cancer in an Asian po... GWASCAT 21242260 Detail
0.124 colorectal cancer A recent genome-wide association study has identified a new genetic variant rs77... BeFree 23555006 Detail
0.003 Colonic Neoplasms [We found a novel susceptible locus in SLC22A3 that contributes to the risk of d... GAD 21242260 Detail
0.004 colorectal carcinoma A recent genome-wide association study has identified a new genetic variant rs77... BeFree 23555006 Detail
Annotation

Annotations

DescrptionSourceLinks
Moreover, we found cumulative effects of three genetic factors (rs7758229, rs6983267, and rs4939827 ... DisGeNET Detail
Moreover, we found cumulative effects of three genetic factors (rs7758229, rs6983267, and rs4939827 ... DisGeNET Detail
Common variant in 6q26-q27 is associated with distal colon cancer in an Asian population. DisGeNET Detail
A recent genome-wide association study has identified a new genetic variant rs7758229 in SLC22A3 for... DisGeNET Detail
[We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal colon cancer i... DisGeNET Detail
A recent genome-wide association study has identified a new genetic variant rs7758229 in SLC22A3 for... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs7758229 dbSNP
Genome
hg19
Position
chr6:160,840,252-160,840,252
Variant Type
snv
Reference Allele
G
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs7758229
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2395
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4014
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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