Variant report

Variant	rs2417657
Chromosome Location	chr9:108672738-108672739
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108669187..108678029-chr9:108711816..108723206,29	MCF-7	breast:
2	chr9:108671913..108676613-chr9:108714105..108718467,7	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10114385	0.89[ASN][1000 genomes]
rs10117135	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10123374	0.89[ASN][1000 genomes]
rs10124171	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10733556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733557	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739216	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759153	0.89[ASN][1000 genomes]
rs10759154	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1987248	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2417654	0.83[EUR][1000 genomes]
rs2417662	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2417676	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4507827	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742973	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035203	0.87[EUR][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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108664800-108673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:108670800-108673600	Weak transcription	NHEK	skin
3	chr9:108670800-108673800	Weak transcription	HMEC	breast
4	chr9:108670800-108674000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:108672200-108674400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr9:108672200-108675400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:108672400-108673000	Enhancers	Fetal Muscle Leg	muscle
8	chr9:108672400-108673200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:108672400-108674600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:108672400-108674600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr9:108672400-108674600	Enhancers	Psoas Muscle	Psoas
12	chr9:108672400-108674800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr9:108672400-108675400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr9:108672400-108675400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:108672400-108676000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:108672600-108673200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:108672600-108673400	Enhancers	A549	lung
18	chr9:108672600-108673600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:108672600-108673800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:108672600-108675200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:108672600-108675400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:108672600-108675400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:108672600-108675600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:108672600-108677000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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