Variant report

Variant	rs61738524
Chromosome Location	chr3:52402778-52402779
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	POLR2A	chr3:52402737-52402850	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:52402771-52402780	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52391704..52393563-chr3:52402367..52404938,2	MCF-7	breast:
2	chr3:52400970..52402826-chr3:52442987..52445575,2	K562	blood:
3	chr3:52401882..52403404-chr3:52567843..52570372,2	K562	blood:

Variant related genes	Relation type
ENSG00000239557	TF binding region
ENSG00000163930	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17052095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28758860	0.95[AFR][1000 genomes]
rs5743838	1.00[AMR][1000 genomes]
rs7615736	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
2	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:52375400-52405600	Strong transcription	Lung	lung
4	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52377000-52406600	Strong transcription	Liver	Liver
6	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
13	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52381400-52407400	Weak transcription	NHLF	lung
18	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
19	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:52384600-52406200	Weak transcription	GM12878-XiMat	blood
21	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
22	chr3:52386000-52406600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:52388600-52403400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:52390400-52403200	Strong transcription	Spleen	Spleen
25	chr3:52390400-52405600	Weak transcription	Fetal Brain Female	brain
26	chr3:52392200-52406400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:52392600-52406600	Strong transcription	Primary T cells from cord blood	blood
28	chr3:52393000-52406400	Strong transcription	Thymus	Thymus
29	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:52393600-52404600	Strong transcription	Primary B cells from cord blood	blood
31	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
32	chr3:52395200-52407200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
35	chr3:52396000-52404200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:52397400-52407400	Weak transcription	Fetal Lung	lung
37	chr3:52397600-52403400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:52397600-52403800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52398000-52407400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
42	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:52399200-52402800	Weak transcription	Aorta	Aorta
44	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:52399600-52403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:52399600-52404800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52399800-52402800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:52399800-52403800	Enhancers	Brain Substantia Nigra	brain
49	chr3:52400000-52403600	Genic enhancers	Brain Angular Gyrus	brain
50	chr3:52400200-52403400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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