Variant report

Variant	rs73455307
Chromosome Location	chr9:72288550-72288551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr9:72286221-72288597	SK-N-SH	brain:	n/a	chr9:72286908-72286918 chr9:72287103-72287113
2	REST	chr9:72286012-72288556	H1-neurons	neurons:	n/a	chr9:72287119-72287126 chr9:72288032-72288045 chr9:72287792-72287806

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72287056..72289421-chr9:72373634..72375235,2	MCF-7	breast:
2	chr9:72286195..72289118-chr9:72373474..72376010,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf135-2	chr9:72287665-72288629	ENSG00000261447.1

Variant related genes	Relation type
APBA1	TF binding region
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17083983	0.86[EUR][1000 genomes]
rs4744926	0.90[EUR][1000 genomes]
rs6559662	0.82[EUR][1000 genomes]
rs7034520	0.90[EUR][1000 genomes]
rs7049167	0.90[EUR][1000 genomes]
rs73453580	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73453583	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7858154	0.90[EUR][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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3389299	chr9:72286157-72289005	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72286200-72288600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:72286400-72288600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr9:72286600-72288600	Active TSS	Brain Anterior Caudate	brain
4	chr9:72286600-72288600	Active TSS	Fetal Brain Female	brain
5	chr9:72287000-72288600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:72287600-72288600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:72287600-72288600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:72287800-72288600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr9:72288000-72288600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:72288000-72288600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:72288000-72288600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:72288000-72288600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr9:72288000-72288600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:72288000-72288600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:72288000-72288600	Flanking Active TSS	Osteobl	bone
16	chr9:72288000-72289200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:72288200-72288600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:72288200-72288600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:72288200-72288600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr9:72288200-72288600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:72288200-72288600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:72288200-72288600	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr9:72288200-72288600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr9:72288200-72288600	Flanking Active TSS	Fetal Heart	heart
25	chr9:72288400-72288600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:72288400-72288600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr9:72288400-72288600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:72288400-72288600	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr9:72288400-72288600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr9:72288400-72288600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr9:72288400-72288600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:72288400-72288600	Enhancers	Adipose Nuclei	Adipose
33	chr9:72288400-72288600	Enhancers	Liver	Liver
34	chr9:72288400-72288600	Enhancers	Brain Angular Gyrus	brain
35	chr9:72288400-72288600	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr9:72288400-72288600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr9:72288400-72288600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:72288400-72288600	Enhancers	Colon Smooth Muscle	Colon
39	chr9:72288400-72288600	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:72288400-72288600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr9:72288400-72288600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr9:72288400-72288600	Active TSS	Fetal Brain Male	brain
43	chr9:72288400-72288600	Enhancers	Fetal Intestine Large	intestine
44	chr9:72288400-72288600	Weak transcription	Ovary	ovary
45	chr9:72288400-72288600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr9:72288400-72288600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr9:72288400-72288600	Enhancers	Rectal Smooth Muscle	rectum
48	chr9:72288400-72288600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr9:72288400-72288600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr9:72288400-72288600	Enhancers	Skeletal Muscle Female	skeletal muscle

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