Variant report

Variant	rs9396254
Chromosome Location	chr6:56893879-56893880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56882958..56887865-chr6:56889010..56894345,6	K562	blood:
2	chr6:56881940..56886581-chr6:56889010..56894702,6	K562	blood:
3	chr6:56892983..56895727-chr6:56899687..56901813,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1002996	0.86[JPT][hapmap]
rs1040461	0.86[JPT][hapmap]
rs10498814	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12175661	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13205191	0.96[EUR][1000 genomes]
rs1556245	0.86[JPT][hapmap]
rs16888268	0.96[EUR][1000 genomes]
rs16888316	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs17758527	0.96[EUR][1000 genomes]
rs17758663	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1839837	0.96[EUR][1000 genomes]
rs1901382	0.82[ASN][1000 genomes]
rs1993118	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2306011	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28498151	0.96[EUR][1000 genomes]
rs3757296	0.86[JPT][hapmap]
rs4510664	0.80[AMR][1000 genomes]
rs4576249	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57994994	0.96[EUR][1000 genomes]
rs58099889	0.96[EUR][1000 genomes]
rs58332182	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59106338	0.96[EUR][1000 genomes]
rs60401134	0.96[EUR][1000 genomes]
rs60910121	0.91[EUR][1000 genomes]
rs61740375	0.86[AMR][1000 genomes]
rs62411412	0.88[EUR][1000 genomes]
rs62411417	0.91[EUR][1000 genomes]
rs62411418	0.91[EUR][1000 genomes]
rs62411419	0.91[EUR][1000 genomes]
rs62411420	0.96[EUR][1000 genomes]
rs62411421	0.96[EUR][1000 genomes]
rs62411422	0.96[EUR][1000 genomes]
rs62411423	0.96[EUR][1000 genomes]
rs62411425	0.96[EUR][1000 genomes]
rs62411430	0.96[EUR][1000 genomes]
rs62415861	0.86[AMR][1000 genomes]
rs62415862	0.82[AMR][1000 genomes]
rs62415863	0.86[AMR][1000 genomes]
rs62415864	0.86[AMR][1000 genomes]
rs62415865	0.83[AMR][1000 genomes]
rs62415878	0.86[AMR][1000 genomes]
rs62415879	0.86[AMR][1000 genomes]
rs62415880	0.86[AMR][1000 genomes]
rs62415883	0.80[AMR][1000 genomes]
rs62415884	0.80[AMR][1000 genomes]
rs62415885	0.86[AMR][1000 genomes]
rs62417377	0.96[EUR][1000 genomes]
rs62417378	0.94[EUR][1000 genomes]
rs62417385	0.94[EUR][1000 genomes]
rs62417430	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6459179	0.86[JPT][hapmap]
rs6907653	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs6932278	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs72867038	0.86[AMR][1000 genomes]
rs7749960	0.86[JPT][hapmap]
rs7766234	0.80[AMR][1000 genomes]
rs7771328	0.86[JPT][hapmap]
rs9296860	0.86[AMR][1000 genomes]
rs9296861	0.86[JPT][hapmap]
rs9296862	0.82[JPT][hapmap]
rs9349842	0.96[EUR][1000 genomes]
rs9349844	0.80[AMR][1000 genomes]
rs9349845	0.86[JPT][hapmap]
rs9357936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357940	0.86[JPT][hapmap]
rs9357941	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs9367700	0.96[EUR][1000 genomes]
rs9367701	0.96[EUR][1000 genomes]
rs9367702	0.96[EUR][1000 genomes]
rs9367706	0.80[AMR][1000 genomes]
rs9367707	0.80[AMR][1000 genomes]
rs9367709	0.80[AMR][1000 genomes]
rs9367710	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9367711	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9367713	0.86[JPT][hapmap]
rs9370550	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9370553	0.96[EUR][1000 genomes]
rs9370554	0.96[EUR][1000 genomes]
rs9370559	0.86[AMR][1000 genomes]
rs9370561	0.80[AMR][1000 genomes]
rs9370562	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs9370563	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9370567	0.86[JPT][hapmap]
rs9382673	0.96[EUR][1000 genomes]
rs9382684	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9382685	0.80[AMR][1000 genomes]
rs9382686	0.86[JPT][hapmap]
rs9382691	0.82[AMR][1000 genomes]
rs9396238	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9396240	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9396245	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9396251	0.92[EUR][1000 genomes]
rs9396252	1.00[CEU][hapmap]
rs9396255	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9396258	0.80[AMR][1000 genomes]
rs9396260	0.86[JPT][hapmap]
rs9396261	0.86[JPT][hapmap]
rs9396263	0.86[JPT][hapmap]
rs9464411	0.96[EUR][1000 genomes]
rs9464412	0.96[EUR][1000 genomes]
rs9464413	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9464418	0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs9464419	0.86[JPT][hapmap]
rs9475757	0.96[EUR][1000 genomes]
rs9475761	0.96[EUR][1000 genomes]
rs9475762	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9475768	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9475774	0.80[AMR][1000 genomes]
rs9475778	0.80[AMR][1000 genomes]
rs9475781	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs9475782	0.86[JPT][hapmap]
rs9475788	0.86[JPT][hapmap]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56878600-56905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:56886000-56894000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:56890600-56894800	Weak transcription	NHDF-Ad	bronchial
4	chr6:56891000-56894000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:56891200-56896200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:56891800-56896200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:56893000-56894000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:56893000-56894400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:56893600-56894400	Enhancers	NHEK	skin
10	chr6:56893600-56894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:56893600-56896400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:56893800-56894400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:56893800-56894400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:56893800-56894400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:56893800-56894800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:56893800-56894800	Weak transcription	Placenta Amnion	Placenta Amnion

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