Variant report

Variant	rs6559516
Chromosome Location	chr9:72007596-72007597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71939060..71941489-chr9:72004680..72008165,4	MCF-7	breast:
2	chr9:72000502..72003339-chr9:72007156..72008716,2	K562	blood:
3	chr9:71938861..71941918-chr9:72004713..72009090,4	MCF-7	breast:
4	chr9:71650223..71652373-chr9:72005112..72007667,2	MCF-7	breast:
5	chr9:72005489..72008452-chr9:72026108..72027745,2	K562	blood:

Variant related genes	Relation type
ENSG00000165060	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10116389	0.87[JPT][hapmap]
rs10780344	0.94[JPT][hapmap]
rs1334312	0.87[JPT][hapmap]
rs1761291	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1929896	0.87[JPT][hapmap]
rs2244720	0.87[JPT][hapmap]
rs2309431	0.87[JPT][hapmap]
rs2777866	0.87[JPT][hapmap]
rs2777878	0.87[JPT][hapmap]
rs2781521	0.87[JPT][hapmap]
rs2781522	0.87[JPT][hapmap]
rs2781526	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3858105	0.81[JPT][hapmap]
rs3934600	0.87[JPT][hapmap]
rs4237230	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs4237234	0.87[JPT][hapmap]
rs4483220	0.87[JPT][hapmap]
rs4484762	0.87[JPT][hapmap]
rs4744886	0.81[JPT][hapmap]
rs4744894	0.87[JPT][hapmap]
rs6559488	0.81[JPT][hapmap]
rs6559489	0.81[JPT][hapmap]
rs6559513	0.86[JPT][hapmap]
rs6559527	0.87[JPT][hapmap]
rs7033674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856778	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
4	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:72002800-72012400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:72003400-72008400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:72003400-72010000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:72003400-72012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:72003400-72012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:72003600-72026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:72006000-72008000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:72006000-72008200	Enhancers	Colon Smooth Muscle	Colon
13	chr9:72006200-72007600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr9:72006200-72007800	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:72006200-72008200	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr9:72006200-72008400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr9:72006200-72013400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:72006400-72007600	Enhancers	Adipose Nuclei	Adipose
19	chr9:72006400-72007600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:72006400-72007600	Genic enhancers	Fetal Stomach	stomach
21	chr9:72006400-72008200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:72006400-72008200	Enhancers	Right Atrium	heart
23	chr9:72006400-72008400	Genic enhancers	Fetal Muscle Leg	muscle
24	chr9:72006400-72008600	Enhancers	Fetal Muscle Trunk	muscle
25	chr9:72006400-72009000	Enhancers	Left Ventricle	heart
26	chr9:72006400-72009000	Enhancers	Psoas Muscle	Psoas
27	chr9:72006400-72010000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:72006400-72010000	Enhancers	Right Ventricle	heart
29	chr9:72006400-72010400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:72006600-72007600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:72006600-72007800	Enhancers	Brain Hippocampus Middle	brain
32	chr9:72006600-72007800	Enhancers	Brain Substantia Nigra	brain
33	chr9:72006600-72007800	Enhancers	Fetal Lung	lung
34	chr9:72006600-72008000	Enhancers	Brain Cingulate Gyrus	brain
35	chr9:72006600-72008000	Enhancers	HSMMtube	muscle
36	chr9:72006600-72008200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr9:72006800-72007600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:72006800-72007600	Enhancers	Fetal Kidney	kidney
39	chr9:72006800-72007600	Strong transcription	Gastric	stomach
40	chr9:72006800-72007800	Genic enhancers	Ovary	ovary
41	chr9:72006800-72008200	Enhancers	Spleen	Spleen
42	chr9:72006800-72010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:72007000-72012800	Weak transcription	Esophagus	oesophagus
44	chr9:72007200-72007600	Weak transcription	Pancreas	Pancrea
45	chr9:72007200-72010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:72007400-72007600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr9:72007400-72007800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:72007400-72007800	Enhancers	Brain Anterior Caudate	brain
49	chr9:72007400-72008000	Transcr. at gene 5' and 3'	Fetal Heart	heart
50	chr9:72007400-72008600	Weak transcription	H9 Cell Line	embryonic stem cell

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