Variant report

Variant	rs56074205
Chromosome Location	chr17:20132227-20132228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20057342..20059768-chr17:20130709..20132708,3	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55939726	0.85[EUR][1000 genomes]
rs56002404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56009494	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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034568	0.88[AMR][1000 genomes];0.94[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[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[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830177	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72830178	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830191	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830194	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830197	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830202	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72832504	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72832506	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72832508	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72832515	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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1065363	chr17:20118499-20162888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1059774	chr17:20118499-20163560	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20109600-20135200	Weak transcription	Gastric	stomach
2	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
3	chr17:20115400-20135000	Weak transcription	Fetal Intestine Small	intestine
4	chr17:20115600-20132800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr17:20118600-20134200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:20125200-20144000	Weak transcription	Small Intestine	intestine
7	chr17:20126400-20134000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:20127200-20132800	Enhancers	Brain Cingulate Gyrus	brain
9	chr17:20128800-20157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:20129000-20134600	Weak transcription	Colonic Mucosa	Colon
11	chr17:20129000-20138600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:20129200-20133000	Weak transcription	Ovary	ovary
13	chr17:20129200-20135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:20129200-20137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:20129200-20161600	Weak transcription	Fetal Brain Female	brain
16	chr17:20129600-20161600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:20130000-20132400	Enhancers	Osteobl	bone
18	chr17:20130200-20133200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:20130400-20132600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:20130400-20135400	Weak transcription	Pancreas	Pancrea
21	chr17:20130600-20132400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:20130600-20132400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr17:20130600-20134400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:20130600-20135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:20130600-20135200	Weak transcription	Lung	lung
26	chr17:20130600-20135400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr17:20130600-20135400	Weak transcription	Brain Germinal Matrix	brain
28	chr17:20130600-20135400	Weak transcription	Esophagus	oesophagus
29	chr17:20130600-20135400	Weak transcription	Left Ventricle	heart
30	chr17:20130600-20135400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:20130600-20139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:20130600-20139000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr17:20130600-20139200	Weak transcription	Fetal Muscle Leg	muscle
34	chr17:20130600-20139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:20130600-20141600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:20130600-20161200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:20130600-20170000	Weak transcription	K562	blood
38	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr17:20130800-20132600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:20130800-20132800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr17:20130800-20133000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:20130800-20134000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr17:20130800-20135200	Weak transcription	Fetal Stomach	stomach
44	chr17:20130800-20135600	Weak transcription	Primary T cells from cord blood	blood
45	chr17:20130800-20135800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr17:20130800-20135800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr17:20130800-20136400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr17:20130800-20136400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr17:20130800-20139800	Weak transcription	Colon Smooth Muscle	Colon
50	chr17:20130800-20140400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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