Variant report

Variant	rs2417660
Chromosome Location	chr9:108680292-108680293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108674993..108676836-chr9:108680080..108681610,2	MCF-7	breast:
2	chr9:108677046..108679182-chr9:108680065..108682717,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10115085	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs10117602	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs10120538	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs10759149	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759150	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759151	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759152	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816353	0.93[ASN][1000 genomes]
rs10978340	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978359	0.84[ASN][1000 genomes]
rs16925032	0.87[CEU][hapmap]
rs1961970	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1987136	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987247	0.99[ASN][1000 genomes]
rs2417644	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2417658	0.97[ASN][1000 genomes]
rs2417659	0.93[ASN][1000 genomes]
rs3884524	0.94[ASN][1000 genomes]
rs4598317	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4742967	0.80[EUR][1000 genomes]
rs4742969	0.81[EUR][1000 genomes]
rs4742974	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742975	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7025973	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs7030289	0.90[ASN][1000 genomes]
rs7040788	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs7043384	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72732742	0.94[ASN][1000 genomes]
rs7851747	0.97[ASN][1000 genomes]
rs7856876	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108674000-108683600	Weak transcription	Left Ventricle	heart
2	chr9:108674400-108683000	Weak transcription	Fetal Heart	heart
3	chr9:108674600-108683600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:108675400-108680800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:108676600-108682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:108677000-108680400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:108677400-108680600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:108677600-108680600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:108677600-108680600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:108677600-108680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:108680200-108680400	Enhancers	HMEC	breast
12	chr9:108680200-108680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:108680200-108680800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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