Variant report

Variant	rs6559478
Chromosome Location	chr9:71957472-71957473
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71938497..71941433-chr9:71956762..71962911,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10735537	0.99[ASN][1000 genomes]
rs10735538	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867360	0.83[AMR][1000 genomes]
rs10867367	0.83[AMR][1000 genomes]
rs11791211	0.80[ASN][1000 genomes]
rs13287458	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13292207	0.83[AMR][1000 genomes]
rs1339544	0.81[ASN][1000 genomes]
rs1931555	0.99[ASN][1000 genomes]
rs3934321	1.00[ASN][1000 genomes]
rs4237229	0.99[ASN][1000 genomes]
rs4341224	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4382537	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515616	0.99[ASN][1000 genomes]
rs4537363	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744566	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744881	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744883	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559480	0.93[ASN][1000 genomes]
rs7021089	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027671	0.81[ASN][1000 genomes]
rs7028837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033121	0.99[ASN][1000 genomes]
rs7043840	0.99[ASN][1000 genomes]
rs7044101	0.99[ASN][1000 genomes]
rs7045431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852930	0.83[AMR][1000 genomes]
rs7861213	0.92[ASN][1000 genomes]
rs7868245	0.94[ASN][1000 genomes]
rs7875734	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71947000-71958000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:71947200-71962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:71948800-71962000	Weak transcription	Pancreas	Pancrea
4	chr9:71950600-71959400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:71950800-71959400	Weak transcription	Lung	lung
6	chr9:71955000-71957600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:71955000-71957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:71955000-71959200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:71955000-71959400	Weak transcription	Right Atrium	heart
10	chr9:71955000-71961600	Weak transcription	Right Ventricle	heart
11	chr9:71955000-71961800	Weak transcription	HMEC	breast
12	chr9:71955000-71962000	Weak transcription	Gastric	stomach
13	chr9:71955200-71959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:71955400-71957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:71955400-71957600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:71955400-71957600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:71955400-71959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:71955400-71981800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:71955600-71957800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:71955600-71957800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:71955600-71958000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:71955600-71959400	Weak transcription	Left Ventricle	heart
23	chr9:71955600-71962000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:71955800-71957600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:71955800-71959400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:71955800-71959600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr9:71955800-71959800	Enhancers	Fetal Heart	heart
28	chr9:71956200-71959200	Weak transcription	Ovary	ovary
29	chr9:71956800-71957600	Weak transcription	Psoas Muscle	Psoas
30	chr9:71957200-71959800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:71957400-71958000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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