Variant report

Variant	rs590656
Chromosome Location	chr6:70967712-70967713
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:70967660-70967878	MCF10A-Er-Src	breast:	n/a	chr6:70967734-70967744 chr6:70967735-70967743 chr6:70967734-70967744 chr6:70967735-70967742 chr6:70967733-70967745 chr6:70967735-70967743
2	FOS	chr6:70967587-70967881	MCF10A-Er-Src	breast:	n/a	chr6:70967734-70967744 chr6:70967735-70967743 chr6:70967734-70967744 chr6:70967735-70967742 chr6:70967733-70967745 chr6:70967735-70967743
3	EP300	chr6:70967515-70967861	SK-N-SH_RA	brain:	n/a	chr6:70967735-70967744
4	GATA3	chr6:70967547-70968089	SK-N-SH	brain:	n/a	chr6:70967917-70967924 chr6:70967913-70967929 chr6:70967910-70967931 chr6:70967733-70967742 chr6:70967917-70967924 chr6:70967913-70967929 chr6:70967917-70967924 chr6:70967902-70967910 chr6:70967900-70967913
5	GATA3	chr6:70967426-70968102	SK-N-SH	brain:	n/a	chr6:70967917-70967924 chr6:70967913-70967929 chr6:70967910-70967931 chr6:70967733-70967742 chr6:70967917-70967924 chr6:70967913-70967929 chr6:70967917-70967924 chr6:70967902-70967910 chr6:70967900-70967913
6	FOS	chr6:70967550-70967840	MCF10A-Er-Src	breast:	n/a	chr6:70967734-70967744 chr6:70967735-70967743 chr6:70967734-70967744 chr6:70967735-70967742 chr6:70967733-70967745 chr6:70967735-70967743

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70954782..70956814-chr6:70966578..70968796,2	K562	blood:

Variant related genes	Relation type
COL9A1	TF binding region
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1135056	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs113979	0.84[AMR][1000 genomes]
rs1200579	0.85[MEX][hapmap]
rs1200580	0.84[MEX][hapmap]
rs1711729	0.95[EUR][1000 genomes]
rs2024730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2076816	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182999	1.00[CHB][hapmap];0.99[ASN][1000 genomes]
rs500457	0.82[AMR][1000 genomes]
rs506908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507676	0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs510423	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs519068	0.89[MEX][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs528080	0.84[AMR][1000 genomes]
rs534258	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535308	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs538588	0.99[ASN][1000 genomes]
rs544179	0.85[MEX][hapmap]
rs546628	0.80[AMR][1000 genomes]
rs550675	0.84[MEX][hapmap]
rs555663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919444	0.99[ASN][1000 genomes]
rs701686	0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs701688	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs701689	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs701690	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs701693	0.80[MEX][hapmap];0.81[AMR][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	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70952200-70980400	Weak transcription	Fetal Stomach	stomach
2	chr6:70952200-70990000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:70952600-70980400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:70952800-70989800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:70955200-70971000	Weak transcription	Fetal Kidney	kidney
6	chr6:70961200-70968000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:70962000-70983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:70965200-70991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:70965400-70969200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:70967600-70967800	Enhancers	Fetal Lung	lung

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