Variant report

Variant	rs9546946
Chromosome Location	chr13:85509470-85509471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12865607	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12876319	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17332066	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34795966	0.89[ASN][1000 genomes]
rs4294708	0.99[ASN][1000 genomes]
rs7335895	0.94[ASN][1000 genomes]
rs7999904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319096	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9319098	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9531697	0.89[ASN][1000 genomes]
rs9546940	0.87[AMR][1000 genomes]
rs9546945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9546948	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9546956	0.96[ASN][1000 genomes]
rs9546958	0.94[ASN][1000 genomes]
rs9546962	0.94[ASN][1000 genomes]
rs9547001	0.89[ASN][1000 genomes]
rs9547005	0.89[ASN][1000 genomes]
rs9547030	0.90[ASN][1000 genomes]
rs9565980	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9565983	0.96[ASN][1000 genomes]
rs9575679	0.91[ASN][1000 genomes]
rs9575680	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9575688	0.94[ASN][1000 genomes]
rs9575689	0.94[ASN][1000 genomes]
rs9602596	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949402	chr13:84675752-85606846	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv900702	chr13:85276978-85605946	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv900703	chr13:85337948-85582307	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv832667	chr13:85422787-85557377	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1041062	chr13:85457391-85531111	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv900704	chr13:85478855-85651739	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv562562	chr13:85482828-85538474	Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv471161	chr13:85497445-85628777	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv430595	chr13:85499399-85566699	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv916866	chr13:85505771-86241562	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv900705	chr13:85505994-85598986	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:85499800-85526600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:85508400-85516000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:85508800-85509600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:85508800-85509600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:85508800-85509800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:85509000-85509600	Active TSS	Primary hematopoietic stem cells	blood
7	chr13:85509000-85509600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:85509000-85509600	Active TSS	Duodenum Mucosa	Duodenum
9	chr13:85509000-85509600	Active TSS	A549	lung
10	chr13:85509000-85509600	Active TSS	NHLF	lung
11	chr13:85509200-85509600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr13:85509200-85509600	Active TSS	Colon Smooth Muscle	Colon
13	chr13:85509400-85509600	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr13:85509400-85509600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr13:85509400-85509600	Enhancers	NHEK	skin

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