Variant report

Variant	rs6091754
Chromosome Location	chr20:52442535-52442536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57183000..57185082-chr20:52441701..52443951,2	MCF-7	breast:
2	chr20:52440503..52443336-chr20:55849623..55851962,2	MCF-7	breast:
3	chr20:45984957..45987024-chr20:52440413..52442622,2	MCF-7	breast:
4	chr20:52437756..52442590-chr20:55839801..55843597,5	MCF-7	breast:
5	chr17:56707305..56708975-chr20:52440122..52442979,2	MCF-7	breast:
6	chr16:81715301..81716813-chr20:52442406..52444099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000224738	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11906821	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs16998448	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4395298	1.00[EUR][1000 genomes]
rs4419278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4452218	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4452219	1.00[EUR][1000 genomes]
rs4574165	1.00[EUR][1000 genomes]
rs4597593	0.93[EUR][1000 genomes]
rs6091749	0.87[EUR][1000 genomes]
rs6091750	0.93[EUR][1000 genomes]
rs6091751	0.93[EUR][1000 genomes]
rs6091752	0.93[EUR][1000 genomes]
rs6097603	0.93[EUR][1000 genomes]
rs6097604	0.93[EUR][1000 genomes]
rs6097605	0.93[EUR][1000 genomes]
rs6097606	1.00[MEX][hapmap]
rs6097607	0.93[EUR][1000 genomes]
rs6097608	0.93[EUR][1000 genomes]
rs6097609	0.93[EUR][1000 genomes]
rs6097610	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097611	1.00[AFR][1000 genomes]
rs6097612	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6097613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097614	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097619	0.83[EUR][1000 genomes]
rs73272060	0.93[EUR][1000 genomes]
rs73272062	0.93[EUR][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52437600-52442600	Weak transcription	Pancreas	Pancrea
3	chr20:52440000-52442600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:52440000-52444800	Weak transcription	Thymus	Thymus
5	chr20:52440800-52445400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52441000-52443000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:52441000-52445000	Enhancers	Fetal Stomach	stomach
8	chr20:52441200-52446000	Enhancers	HepG2	liver
9	chr20:52441400-52442600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr20:52441400-52443200	Weak transcription	Fetal Intestine Small	intestine
11	chr20:52441400-52443200	Enhancers	A549	lung
12	chr20:52441400-52443800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr20:52441600-52444600	Weak transcription	Colon Smooth Muscle	Colon
14	chr20:52441600-52445200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr20:52441800-52443400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:52441800-52444400	Enhancers	Fetal Lung	lung
17	chr20:52442000-52443600	Weak transcription	Small Intestine	intestine
18	chr20:52442000-52444600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr20:52442200-52443400	Weak transcription	Primary T cells from cord blood	blood
20	chr20:52442200-52443600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr20:52442400-52442800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:52442400-52443400	Weak transcription	Fetal Kidney	kidney
23	chr20:52442400-52443600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr20:52442400-52444800	Weak transcription	Stomach Mucosa	stomach
25	chr20:52442400-52445000	Weak transcription	Duodenum Mucosa	Duodenum

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