Variant report

Variant	rs559801068
Chromosome Location	chr3:52031397-52031398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:52031244-52031484	HepG2	liver:	n/a	n/a
2	RCOR1	chr3:52031269-52031504	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52001556..52005448-chr3:52028528..52032420,5	MCF-7	breast:
2	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
3	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:

Variant related genes	Relation type
RPL29	TF binding region
ENSG00000114767	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000114779	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
11	nsv236961	chr3:52030637-52035392	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52030000-52031600	Weak transcription	K562	blood
2	chr3:52030000-52031800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:52030000-52031800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:52030000-52031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:52030000-52031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:52030000-52031800	Weak transcription	HMEC	breast
7	chr3:52030000-52032000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:52030000-52032000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52030000-52032000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:52030000-52032000	Weak transcription	HSMM	muscle
11	chr3:52030000-52032200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52030000-52034200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:52030000-52034400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52030000-52035600	Weak transcription	Esophagus	oesophagus
15	chr3:52030200-52031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:52030200-52031800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:52030200-52031800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:52030200-52031800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:52030200-52031800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:52030200-52031800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52030200-52031800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:52030200-52031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:52030200-52031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:52030200-52031800	Weak transcription	NHEK	skin
25	chr3:52030200-52032000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:52030200-52032000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52030200-52032000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:52030200-52032000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:52030200-52032000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:52030200-52032000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:52030200-52032000	Weak transcription	A549	lung
32	chr3:52030200-52032000	Weak transcription	HUVEC	blood vessel
33	chr3:52030200-52035400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:52030200-52035400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:52030200-52038600	Weak transcription	Fetal Kidney	kidney
36	chr3:52030400-52032000	Weak transcription	Fetal Intestine Large	intestine
37	chr3:52030400-52033200	Enhancers	HepG2	liver
38	chr3:52030400-52034200	Weak transcription	Placenta	Placenta
39	chr3:52030400-52035400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:52030400-52035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:52030400-52035400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:52030400-52035400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:52030400-52035400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:52030400-52035400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52030400-52035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:52030400-52035400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:52030400-52035400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:52030400-52035400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:52030400-52035400	Weak transcription	Fetal Thymus	thymus
50	chr3:52030400-52035400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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