Variant report

Variant	rs11659841
Chromosome Location	chr18:25786880-25786881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11662215	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12966227	0.90[ASN][1000 genomes]
rs1988880	0.81[ASN][1000 genomes]
rs1990414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990416	0.81[AFR][1000 genomes]
rs2109627	1.00[ASN][1000 genomes]
rs2159641	0.94[ASN][1000 genomes]
rs2191634	0.94[ASN][1000 genomes]
rs2215502	0.84[ASN][1000 genomes]
rs713198	0.80[JPT][hapmap]
rs8085425	0.88[ASN][1000 genomes]
rs9945455	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9948832	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv9622	chr18:25749905-26032816	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Periodontal disease-related phenotypes	24347629	GWAS catalog

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25784600-25788400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:25784800-25788000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:25784800-25788000	Weak transcription	Aorta	Aorta
4	chr18:25784800-25788200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr18:25785000-25788600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:25785000-25788600	Weak transcription	Osteobl	bone

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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

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