Variant report

Variant	rs2417658
Chromosome Location	chr9:108674392-108674393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:108672760..108675101-chr9:110098994..110101048,2	MCF-7	breast:
2	chr9:108673478..108676397-chr9:109721391..109723728,2	MCF-7	breast:
3	chr9:108669187..108678029-chr9:108711816..108723206,29	MCF-7	breast:
4	chr9:108672824..108675555-chr9:108676544..108678880,2	MCF-7	breast:
5	chr9:108673529..108676504-chr9:109332780..109334808,2	MCF-7	breast:
6	chr9:108663819..108664519-chr9:108673345..108674675,3	MCF-7	breast:
7	chr9:108674312..108676473-chr9:108677250..108680180,2	K562	blood:
8	chr9:108671913..108676613-chr9:108714105..108718467,7	MCF-7	breast:
9	chr9:108643116..108645667-chr9:108673078..108675664,2	MCF-7	breast:

No data

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10759149	0.97[ASN][1000 genomes]
rs10759150	0.98[ASN][1000 genomes]
rs10759151	0.99[ASN][1000 genomes]
rs10759152	1.00[ASN][1000 genomes]
rs10816353	0.93[ASN][1000 genomes]
rs10978340	0.94[ASN][1000 genomes]
rs10978359	0.83[ASN][1000 genomes]
rs1961970	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1987136	0.97[ASN][1000 genomes]
rs1987247	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417659	0.92[ASN][1000 genomes]
rs2417660	0.97[ASN][1000 genomes]
rs3884524	0.93[ASN][1000 genomes]
rs4742974	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742975	0.84[ASN][1000 genomes]
rs7030289	0.93[ASN][1000 genomes]
rs7043384	0.95[ASN][1000 genomes]
rs72732742	0.93[ASN][1000 genomes]
rs7851747	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7856876	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108672200-108674400	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr9:108672200-108675400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:108672400-108674600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:108672400-108674600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr9:108672400-108674600	Enhancers	Psoas Muscle	Psoas
6	chr9:108672400-108674800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr9:108672400-108675400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr9:108672400-108675400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:108672400-108676000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:108672600-108675200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:108672600-108675400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:108672600-108675400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:108672600-108675600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:108672600-108677000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:108672800-108674400	Enhancers	HepG2	liver
16	chr9:108672800-108675200	Enhancers	Brain Anterior Caudate	brain
17	chr9:108673000-108674400	Enhancers	Fetal Heart	heart
18	chr9:108673000-108675400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:108673000-108677800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr9:108673200-108674400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr9:108673200-108675000	Enhancers	Brain Hippocampus Middle	brain
22	chr9:108673200-108675200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr9:108673200-108675200	Enhancers	Brain Substantia Nigra	brain
24	chr9:108673200-108675400	Enhancers	Fetal Kidney	kidney
25	chr9:108673200-108675800	Enhancers	Stomach Smooth Muscle	stomach
26	chr9:108673200-108676200	Enhancers	Hela-S3	cervix
27	chr9:108673200-108676600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:108673400-108674400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr9:108673400-108675000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr9:108673400-108675400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:108673400-108675400	Enhancers	Fetal Muscle Leg	muscle
32	chr9:108673400-108675400	Flanking Active TSS	A549	lung
33	chr9:108673400-108676600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:108673600-108674400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr9:108673600-108674400	Enhancers	NH-A	brain
36	chr9:108673600-108674400	Enhancers	Osteobl	bone
37	chr9:108673600-108674600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr9:108673600-108674600	Enhancers	Placenta	Placenta
39	chr9:108673600-108674800	Enhancers	Aorta	Aorta
40	chr9:108673600-108675000	Enhancers	Brain Angular Gyrus	brain
41	chr9:108673600-108675400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:108673600-108675400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr9:108673600-108675800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr9:108673600-108676000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:108673600-108676000	Enhancers	NHEK	skin
46	chr9:108673800-108674600	Enhancers	HSMM	muscle
47	chr9:108673800-108675400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:108673800-108675400	Enhancers	Colon Smooth Muscle	Colon
49	chr9:108673800-108675600	Enhancers	Adipose Nuclei	Adipose
50	chr9:108673800-108675600	Enhancers	Rectal Smooth Muscle	rectum

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