Variant report

Variant	rs6559854
Chromosome Location	chr9:72538868-72538869
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	chr9:72533081..72534901-chr9:72537488..72539273,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1027283	0.83[ASN][1000 genomes]
rs1027284	0.82[ASN][1000 genomes]
rs10735572	0.89[ASN][1000 genomes]
rs10780718	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10780720	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10780724	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868248	0.82[JPT][hapmap]
rs10868291	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868299	0.89[ASN][1000 genomes]
rs10868327	0.88[ASN][1000 genomes]
rs1121607	0.89[ASN][1000 genomes]
rs1121608	0.89[ASN][1000 genomes]
rs1389125	0.83[ASN][1000 genomes]
rs1473520	0.81[ASN][1000 genomes]
rs1493046	0.86[ASN][1000 genomes]
rs1493047	0.89[ASN][1000 genomes]
rs1493051	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1493054	0.85[EUR][1000 genomes]
rs1542769	0.83[ASN][1000 genomes]
rs1565685	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1565686	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1586914	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1873825	0.87[ASN][1000 genomes]
rs1907956	0.89[ASN][1000 genomes]
rs1907959	0.89[ASN][1000 genomes]
rs1976234	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2035922	0.87[ASN][1000 genomes]
rs4413835	0.83[ASN][1000 genomes]
rs4445287	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4487845	0.82[ASN][1000 genomes]
rs4490905	0.82[ASN][1000 genomes]
rs4574911	0.83[ASN][1000 genomes]
rs4744959	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60125094	0.86[EUR][1000 genomes]
rs6559850	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7019025	0.87[ASN][1000 genomes]
rs7025044	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7029606	0.89[ASN][1000 genomes]
rs7035415	0.82[ASN][1000 genomes]
rs7037671	0.89[ASN][1000 genomes]
rs7847934	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7863165	0.89[ASN][1000 genomes]
rs7869305	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs870011	0.82[ASN][1000 genomes]
rs902964	0.86[ASN][1000 genomes]
rs931500	0.81[ASN][1000 genomes]
rs996375	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv893439	chr9:72500956-72568962	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1043276	chr9:72522231-72571726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72514000-72539600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:72537800-72539200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:72538000-72539600	Enhancers	H9 Cell Line	embryonic stem cell
4	chr9:72538600-72539000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:72538600-72539200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:72538600-72539200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:72538800-72539200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:72538800-72539400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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