Variant report

Variant	rs62560873
Chromosome Location	chr9:99839186-99839187
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:38487559..38489078-chr9:99839080..99841852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229511	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10114720	0.83[ASN][1000 genomes]
rs10118886	0.83[ASN][1000 genomes]
rs10118923	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10123754	0.83[ASN][1000 genomes]
rs10123757	0.83[ASN][1000 genomes]
rs10739289	0.83[ASN][1000 genomes]
rs10739296	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759400	0.82[ASN][1000 genomes]
rs10759406	0.83[ASN][1000 genomes]
rs10759417	0.85[ASN][1000 genomes]
rs10759420	0.85[ASN][1000 genomes]
rs10816926	0.83[ASN][1000 genomes]
rs10816951	0.81[ASN][1000 genomes]
rs10816962	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10816963	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10816964	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10816981	0.85[ASN][1000 genomes]
rs10816984	0.85[ASN][1000 genomes]
rs10816994	0.85[ASN][1000 genomes]
rs10817013	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10980326	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10980346	0.85[ASN][1000 genomes]
rs10980396	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12236690	0.81[ASN][1000 genomes]
rs12376012	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12376575	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12377546	0.85[ASN][1000 genomes]
rs13285842	0.92[ASN][1000 genomes]
rs15394	0.83[ASN][1000 genomes]
rs16924211	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2004336	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34342973	0.85[ASN][1000 genomes]
rs4367680	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4501700	0.84[ASN][1000 genomes]
rs4510972	0.85[ASN][1000 genomes]
rs59995818	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6477844	0.82[ASN][1000 genomes]
rs7023974	0.83[ASN][1000 genomes]
rs7038926	0.83[ASN][1000 genomes]
rs7039198	0.83[ASN][1000 genomes]
rs7857836	0.85[ASN][1000 genomes]
rs7873286	0.81[ASN][1000 genomes]
rs9792463	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99835400-99839400	Weak transcription	Fetal Heart	heart
2	chr9:99837800-99841400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:99838200-99840000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:99838200-99840800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:99838400-99839600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr9:99838400-99839600	Bivalent Enhancer	Fetal Stomach	stomach
7	chr9:99838400-99839800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr9:99838600-99839800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr9:99838600-99839800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
10	chr9:99838600-99841200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:99838800-99839200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:99838800-99839200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:99838800-99839200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:99838800-99839400	Bivalent Enhancer	Fetal Brain Female	brain
15	chr9:99838800-99839400	Enhancers	Gastric	stomach
16	chr9:99838800-99839400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:99838800-99839400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr9:99838800-99839600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:99839000-99839200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr9:99839000-99839400	Enhancers	Pancreas	Pancrea
21	chr9:99839000-99839800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:99839000-99840000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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