Variant report

Variant	rs12791787
Chromosome Location	chr11:56610933-56610934
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12416731	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12418598	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786794	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12787988	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12788119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792882	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12808001	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1943640	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4938838	0.81[ASN][1000 genomes]
rs4939087	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4939088	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827526	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7117269	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048328	chr11:56471984-56649908	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv2830406	chr11:56481955-56650124	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv468577	chr11:56503728-56704042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555101	chr11:56503728-56704042	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv469960	chr11:56605222-56704042	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12791787	OR8J1	cis	parietal	SCAN
rs12791787	OR5M11	cis	cerebellum	SCAN
rs12791787	MS4A6E	cis	cerebellum	SCAN
rs12791787	CTNND1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56609000-56611000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:56609000-56611600	Enhancers	Stomach Mucosa	stomach
3	chr11:56609200-56613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:56609200-56614000	Weak transcription	Fetal Kidney	kidney
5	chr11:56609400-56613800	Weak transcription	NHEK	skin
6	chr11:56610200-56613600	Weak transcription	HMEC	breast
7	chr11:56610800-56611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:56610800-56613200	ZNF genes & repeats	A549	lung
9	chr11:56610800-56614400	Weak transcription	Fetal Lung	lung

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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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