Variant report

Variant	rs10780953
Chromosome Location	chr9:73216990-73216991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:73027993..73028866-chr9:73216974..73217674,2	MCF-7	breast:
2	chr9:73027361..73029431-chr9:73215133..73217695,2	MCF-7	breast:
3	chr9:73033647..73036708-chr9:73216290..73219440,5	MCF-7	breast:
4	chr9:72955339..72956157-chr9:73216775..73218041,5	K562	blood:
5	chr9:73216054..73218169-chr9:73220348..73222412,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMC5-9	chr9:73216899-73217010	NONHSAT131818

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10868857	0.92[ASN][1000 genomes]
rs10868858	0.98[ASN][1000 genomes]
rs10868859	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142497	0.86[JPT][hapmap]
rs11142503	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615645	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7865858	0.86[JPT][hapmap];0.81[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	nsv831616	chr9:73077855-73220928	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv614598	chr9:73193371-73218656	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73206600-73227800	Weak transcription	Aorta	Aorta
2	chr9:73213600-73224600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:73214200-73220400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:73215000-73217000	Enhancers	Colon Smooth Muscle	Colon
5	chr9:73215000-73217000	Enhancers	Fetal Muscle Trunk	muscle
6	chr9:73215000-73217600	Enhancers	Ovary	ovary
7	chr9:73215000-73218200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:73215200-73217000	Enhancers	Right Atrium	heart
9	chr9:73215200-73217200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:73215200-73217400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr9:73215200-73217400	Flanking Active TSS	HSMMtube	muscle
12	chr9:73215200-73217800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr9:73215200-73217800	Enhancers	Left Ventricle	heart
14	chr9:73215400-73217000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:73215400-73217400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:73215400-73217400	Flanking Active TSS	HSMM	muscle
17	chr9:73215400-73217800	Enhancers	Fetal Muscle Leg	muscle
18	chr9:73215400-73218000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:73215400-73218000	Enhancers	Fetal Stomach	stomach
20	chr9:73215600-73217000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:73215600-73217400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:73215600-73217400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:73215600-73217400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:73215600-73217400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr9:73215600-73217600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr9:73215600-73217800	Enhancers	Fetal Heart	heart
27	chr9:73215800-73217000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:73215800-73217000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:73215800-73217000	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr9:73215800-73217200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr9:73215800-73217400	Enhancers	Fetal Brain Female	brain
32	chr9:73215800-73217600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr9:73215800-73218000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr9:73215800-73236800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:73216000-73217000	Enhancers	Pancreas	Pancrea
36	chr9:73216000-73217000	Bivalent Enhancer	Stomach Mucosa	stomach
37	chr9:73216000-73217400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr9:73216000-73217400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:73216000-73217400	Enhancers	Brain Germinal Matrix	brain
40	chr9:73216000-73217600	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr9:73216000-73217600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr9:73216000-73227600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:73216200-73217000	Enhancers	Colonic Mucosa	Colon
44	chr9:73216200-73217400	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr9:73216200-73217600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr9:73216200-73217600	Enhancers	Fetal Intestine Small	intestine
47	chr9:73216200-73219000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:73216400-73217400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr9:73216400-73217400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr9:73216400-73217400	Flanking Active TSS	NH-A	brain

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