Variant report

Variant	rs6033819
Chromosome Location	chr20:13745905-13745906
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	chr20:13745856..13749163-chr20:13765224..13767517,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs13039364	0.88[CHB][hapmap]
rs13042637	0.84[ASN][1000 genomes]
rs1547920	0.91[ASN][1000 genomes]
rs1999112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2031933	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2094651	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2209993	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327797	0.88[CHB][hapmap]
rs2423745	0.97[ASN][1000 genomes]
rs2423749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2423750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2423753	0.86[ASN][1000 genomes]
rs3180370	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34449907	0.90[ASN][1000 genomes]
rs34806363	0.90[ASN][1000 genomes]
rs35361761	0.81[ASN][1000 genomes]
rs35632254	0.81[ASN][1000 genomes]
rs3789339	0.84[CEU][hapmap]
rs4813139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4813141	0.84[EUR][1000 genomes]
rs4813142	0.93[ASN][1000 genomes]
rs4814256	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4814258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033809	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6033816	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033821	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6042336	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs6042347	0.89[EUR][1000 genomes]
rs6042351	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042357	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6042362	0.97[ASN][1000 genomes]
rs6074637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6074643	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6074644	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6079154	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs6079156	0.86[CHB][hapmap]
rs6079158	0.88[CHB][hapmap]
rs6079162	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6079165	0.84[ASN][1000 genomes]
rs6079166	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs6079176	0.90[ASN][1000 genomes]
rs6079178	0.90[ASN][1000 genomes]
rs6079181	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6079182	0.86[ASN][1000 genomes]
rs6105162	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6110026	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6110035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134968	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62209178	0.84[ASN][1000 genomes]
rs62209207	0.90[ASN][1000 genomes]
rs68012295	0.91[ASN][1000 genomes]
rs7265467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs754796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription 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	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13693000-13746400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr20:13694400-13748000	Weak transcription	Gastric	stomach
3	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
4	chr20:13713000-13746200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:13713000-13747400	Weak transcription	Right Ventricle	heart
6	chr20:13713000-13748600	Weak transcription	Spleen	Spleen
7	chr20:13722000-13748400	Weak transcription	Aorta	Aorta
8	chr20:13722200-13747800	Weak transcription	Lung	lung
9	chr20:13722200-13748400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:13728400-13746600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:13730200-13748600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:13731400-13747800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:13731600-13747800	Weak transcription	Fetal Intestine Small	intestine
14	chr20:13731600-13748400	Weak transcription	Esophagus	oesophagus
15	chr20:13734000-13763200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr20:13734200-13746200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:13734600-13748000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:13735000-13746200	Weak transcription	Fetal Heart	heart
19	chr20:13736800-13763800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:13737200-13746800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr20:13737600-13746200	Weak transcription	NHLF	lung
22	chr20:13738200-13747400	Weak transcription	Psoas Muscle	Psoas
23	chr20:13738400-13746200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:13740400-13746200	Weak transcription	HMEC	breast
25	chr20:13740600-13746600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr20:13740800-13746000	Weak transcription	Fetal Lung	lung
27	chr20:13740800-13746200	Weak transcription	Fetal Brain Female	brain
28	chr20:13740800-13757600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr20:13741800-13763200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr20:13741800-13763800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr20:13742000-13746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:13742000-13757600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr20:13742000-13757800	Strong transcription	NH-A	brain
34	chr20:13742000-13759000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr20:13742000-13762600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr20:13742200-13746000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr20:13742200-13746400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr20:13742200-13746600	Strong transcription	Adipose Nuclei	Adipose
39	chr20:13742200-13746600	Strong transcription	HepG2	liver
40	chr20:13742200-13763600	Strong transcription	Liver	Liver
41	chr20:13742400-13746200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:13742400-13746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr20:13742400-13746400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:13742400-13749200	Strong transcription	HSMM	muscle
45	chr20:13742400-13763800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr20:13742800-13746600	Strong transcription	NHDF-Ad	bronchial
47	chr20:13742800-13746800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr20:13742800-13746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:13742800-13752400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr20:13743000-13746800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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