Variant report

Variant	rs56002404
Chromosome Location	chr17:20096860-20096861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20096735..20100140-chr17:20107698..20112138,4	K562	blood:
2	chr17:20090600..20093131-chr17:20093995..20097468,3	MCF-7	breast:
3	chr17:20096015..20099683-chr17:20108650..20110634,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs16960662	0.83[EUR][1000 genomes]
rs16960672	0.83[EUR][1000 genomes]
rs55650639	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55814709	0.85[EUR][1000 genomes]
rs55832890	0.85[EUR][1000 genomes]
rs55853482	0.85[EUR][1000 genomes]
rs55854412	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55891925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55939726	0.85[EUR][1000 genomes]
rs56009494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56009515	0.83[EUR][1000 genomes]
rs56020078	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56020655	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034568	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56074205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56186136	0.83[EUR][1000 genomes]
rs56194672	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56208903	0.85[EUR][1000 genomes]
rs56267204	0.85[EUR][1000 genomes]
rs56281769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56301435	0.83[EUR][1000 genomes]
rs56344048	0.83[EUR][1000 genomes]
rs7207672	0.83[EUR][1000 genomes]
rs72830109	0.83[EUR][1000 genomes]
rs72830114	0.83[EUR][1000 genomes]
rs72830123	0.83[EUR][1000 genomes]
rs72830128	0.85[EUR][1000 genomes]
rs72830139	0.84[EUR][1000 genomes]
rs72830141	0.87[EUR][1000 genomes]
rs72830145	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830150	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72830153	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830165	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830177	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72830178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830197	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72832504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72832506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72832508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72832515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72832518	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72832520	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72832522	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1057870	chr17:20079146-20121848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20089000-20097600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:20089600-20098000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:20092600-20097200	Enhancers	Brain Anterior Caudate	brain
4	chr17:20093000-20097800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:20093000-20099600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:20094200-20097200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:20094200-20097800	Enhancers	Brain Substantia Nigra	brain
8	chr17:20094200-20098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:20094200-20098400	Enhancers	Brain Hippocampus Middle	brain
10	chr17:20094200-20103800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:20094200-20105400	Weak transcription	Gastric	stomach
12	chr17:20094600-20097800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:20094600-20099400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:20094600-20101000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr17:20094600-20105400	Weak transcription	K562	blood
16	chr17:20094800-20097200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:20094800-20097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:20094800-20105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:20095000-20097200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:20095200-20101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:20095400-20104800	Weak transcription	HMEC	breast
22	chr17:20095600-20099600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:20096000-20103600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:20096200-20097000	Enhancers	Ovary	ovary
25	chr17:20096200-20097800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:20096200-20100600	Enhancers	Hela-S3	cervix
27	chr17:20096200-20101000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:20096400-20097000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr17:20096400-20097600	Enhancers	Duodenum Mucosa	Duodenum
30	chr17:20096400-20100800	Weak transcription	Aorta	Aorta
31	chr17:20096600-20097400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:20096800-20097000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr17:20096800-20103400	Weak transcription	Brain Angular Gyrus	brain

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