Variant report

Variant	rs17052020
Chromosome Location	chr3:52248575-52248576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52238883..52243786-chr3:52243916..52248823,6	K562	blood:
2	chr3:52244082..52246487-chr3:52247425..52250962,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs28758860	1.00[MEX][hapmap]
rs56990501	1.00[EUR][1000 genomes]
rs5743838	1.00[EUR][1000 genomes]
rs6445259	1.00[EUR][1000 genomes]
rs6784563	1.00[EUR][1000 genomes]
rs6784653	1.00[EUR][1000 genomes]
rs6797786	1.00[EUR][1000 genomes]
rs7611413	1.00[MEX][hapmap]
rs7614535	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs7615736	1.00[MEX][hapmap]
rs7617023	1.00[EUR][1000 genomes]
rs7623076	1.00[EUR][1000 genomes]
rs7625515	1.00[EUR][1000 genomes]
rs7636412	1.00[EUR][1000 genomes]
rs7652984	1.00[EUR][1000 genomes]

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	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
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 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	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:52233600-52249000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:52233600-52249200	Strong transcription	Fetal Muscle Leg	muscle
7	chr3:52233600-52249600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:52233600-52250000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52233600-52250000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:52233600-52250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:52233600-52250200	Strong transcription	Fetal Stomach	stomach
12	chr3:52233800-52249600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:52233800-52250000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:52233800-52250400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:52234400-52249800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:52234600-52249800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:52234600-52249800	Strong transcription	HSMM	muscle
18	chr3:52234600-52249800	Strong transcription	HUVEC	blood vessel
19	chr3:52234600-52250000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:52234800-52251000	Strong transcription	Fetal Brain Female	brain
21	chr3:52235000-52250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:52235200-52249200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:52235200-52249200	Strong transcription	Fetal Kidney	kidney
24	chr3:52235200-52249600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:52235200-52249800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:52235400-52249800	Strong transcription	Brain Cingulate Gyrus	brain
27	chr3:52235400-52250000	Strong transcription	Brain Germinal Matrix	brain
28	chr3:52235400-52250400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:52235600-52248600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:52235600-52250000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:52235800-52249400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:52235800-52249600	Strong transcription	Brain Anterior Caudate	brain
33	chr3:52235800-52249800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:52235800-52249800	Strong transcription	Brain Substantia Nigra	brain
35	chr3:52235800-52249800	Strong transcription	Fetal Thymus	thymus
36	chr3:52235800-52249800	Strong transcription	Dnd41	blood
37	chr3:52235800-52250000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:52235800-52250400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:52236000-52249800	Strong transcription	Primary T cells from cord blood	blood
40	chr3:52236200-52250200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:52236200-52250200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr3:52236200-52250200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52236400-52249400	Strong transcription	Colon Smooth Muscle	Colon
44	chr3:52236400-52249400	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr3:52236400-52249400	Strong transcription	Right Ventricle	heart
46	chr3:52236400-52249600	Strong transcription	Brain Angular Gyrus	brain
47	chr3:52236400-52249800	Strong transcription	Ovary	ovary
48	chr3:52236400-52249800	Strong transcription	Rectal Smooth Muscle	rectum
49	chr3:52236400-52250000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:52236400-52250200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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