Variant report

Variant	rs527417
Chromosome Location	chr15:54052162-54052163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:54050503..54054059-chr15:54055807..54059339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206641	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10467926	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071001	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1107728	0.87[EUR][1000 genomes]
rs1107729	0.87[EUR][1000 genomes]
rs1107730	0.90[EUR][1000 genomes]
rs11633580	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11635018	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11635066	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591101	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12594072	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12915223	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1461423	0.97[ASN][1000 genomes]
rs1841577	0.95[ASN][1000 genomes]
rs1903461	0.82[EUR][1000 genomes]
rs2169344	0.82[EUR][1000 genomes]
rs4776171	0.87[EUR][1000 genomes]
rs690656	0.91[EUR][1000 genomes]
rs7161786	0.90[EUR][1000 genomes]
rs7162653	0.90[EUR][1000 genomes]
rs7164670	0.84[EUR][1000 genomes]
rs7167506	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167726	0.91[EUR][1000 genomes]
rs7172509	0.86[EUR][1000 genomes]
rs7183766	0.89[EUR][1000 genomes]
rs7183817	0.90[EUR][1000 genomes]
rs7183948	0.90[EUR][1000 genomes]
rs8035071	0.86[EUR][1000 genomes]
rs898736	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv833010	chr15:53935652-54099849	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv949528	chr15:54041154-54281981	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54050600-54052200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:54050800-54052200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr15:54050800-54052400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:54051000-54052200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:54051000-54052200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr15:54051000-54052200	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr15:54051000-54052400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:54051200-54052400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:54051400-54052200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr15:54051400-54052200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:54051400-54052200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr15:54051400-54052200	Active TSS	Aorta	Aorta
13	chr15:54051400-54052400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr15:54051600-54052200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:54051600-54052200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:54051600-54052200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:54051600-54052200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
18	chr15:54051600-54052200	Bivalent Enhancer	Left Ventricle	heart
19	chr15:54051600-54052200	Active TSS	Right Atrium	heart
20	chr15:54051600-54052200	Active TSS	HepG2	liver
21	chr15:54051600-54052400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr15:54051800-54052200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:54051800-54052200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:54051800-54052200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
25	chr15:54051800-54052200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:54051800-54052200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:54051800-54052200	Bivalent Enhancer	Adipose Nuclei	Adipose
28	chr15:54051800-54052200	Active TSS	Liver	Liver
29	chr15:54051800-54052200	Active TSS	Brain Germinal Matrix	brain
30	chr15:54051800-54052200	Active TSS	Colonic Mucosa	Colon
31	chr15:54051800-54052200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr15:54051800-54052200	Active TSS	Pancreas	Pancrea
33	chr15:54051800-54052200	Active TSS	Psoas Muscle	Psoas
34	chr15:54051800-54052200	Bivalent/Poised TSS	Right Ventricle	heart
35	chr15:54052000-54052200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

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