Variant report

Variant	rs649057
Chromosome Location	chr9:102234323-102234324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12553249	0.82[ASN][1000 genomes]
rs12553685	0.81[ASN][1000 genomes]
rs1373131	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16918616	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2900171	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57713933	0.82[ASN][1000 genomes]
rs617164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs623874	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs634202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs638261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7863995	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831667	chr9:102068047-102285691	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv6636	chr9:102197504-102242604	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Dental caries	23064961	GWAS catalog
Smooth-surface caries	23470693	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs649057	GALNT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102229000-102235800	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:102230000-102235600	Weak transcription	Fetal Heart	heart
3	chr9:102233800-102235200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:102234000-102235800	Weak transcription	Fetal Brain Female	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links